Bowing as you enter, you remove your shoes once you step inside the door, before you stand on the raised platform, carefully placing them inside the wooden shelves set aside for that purpose. They are replaced by slippers, too small for your big western feet, thick brown leather straps loosely covering the tips of your toes. Your host bows, greets you, and points you towards the desk, where you hand over your passports for inspection and fill out the form. Formalities aside, you follow your host, lugging your cases up narrow wooden stairs, desperately trying not to slip in those so aptly named slippers.

Kyoto’s railway station is a modern architectural marvel, a huge wavy edifice of steel and glass, befitting of the cultural and historic former capital of Japan. But step outside and there is an immediate sense of disappointment. Ugly grey buildings overlooked by the tacky white and red Kyoto tower. Where are the temples, the old wooden buildings, the history, the culture?

The air is tropically hot sticky, the skies grey. September is possibly the worst month to visit Japan. As we try to find our way to the tiny ryokan it begins to rain, a sudden heavy downpour that would be at home in an equatorial nation.

We pass the Higashi Hongan-ji temple complex and a row of tiny sweet shops, traces of old Japan appear amongst the concrete modernity. A tethered dog barks at us in the narrow side street where the Ryokan Murakamiya is hidden away.

We had discovered the Murakamiya in the pages of the Lonely Planet. Although I had spent three years learning Japanese in high school my language skills were basic at best and I hoped that the accommodation would be westerner friendly on this, our first visit to Japan.

The elderly lady who greeted us spoke some English. She told us that she had expected us yesterday. With great shock I realise that I had got the dates wrong. No wonder the staff at our business hotel in Tokyo were confused at our checkout this morning.

Ah, the owner said, it must be the time difference that has confused you. Despite coming from a time zone of only one hour ahead, we all accepted this mutually face saving excuse.

The room is small and basic, toilets and bathrooms shared with other guests. Yukata, or Japanese indoor robes, hang from wooden stands. A low table with two zabuton cushions sits by the curtained window, while a small television plays on top of furniture barely a foot high. Our futons are folded up to one side, ready to be extended for sleeping. There is no air-conditioning and we rely on old fashioned hand fans to cool ourselves down, making it difficult to sleep when we return before the 10 pm curfew.

Baths have to be booked, the deep tub only large enough for one person, the air reeking of kerosene from the heater that keeps the water scorchingly hot. But there is a view outside into the simple Japanese garden, a hint of relaxation.

The Murakamiya is not a great introduction in the world of the Japanese ryokan and indeed I did not fall in love with the country on this trip, but for one small part. The sweet scent of the straw tatami mats fills the warm air. On our next visit to Japan, passing through on a return flight from Europe, I discover the secret to learning to love Japan and carry back our own straw tatami so that its scent may fill our own home.

Less than three years after our first visit to Japan and we have definitely fallen in love with the country. It is April and the cherry blossoms are in bloom. Kanazawa is home to Kenroku-en, the greatest of the three best gardens in Japan, along with many other wonderful sights. It is one of my favourite cities in Japan and this is our first time there.

We rock up to Kanazawa’s train station without a bed for the night, asking for assistance from the very friendly tourist office. They book us into the Ryokan Murataya, a welcoming inn that was quite used to foreign visitors, judging from the posts on their notice board.

Our room is much larger than the previous experience, painted a cheerful green that contrasts beautifully with the wooden frames of the paper shoji screens separating the sections of the room. On the low table is a flask of hot water to make tea, welcome in the chill air of a part of the country still farewelling the last vestiges of winter. We saw snow drifts on the train ride up from Takayama to Kanazawa.

The Murataya is located close to Kanazawa’s downtown area, busy with pedestrians and cars, department stores selling exquisite local pottery. By the river are wooden buildings dating back to the Samurai era, further along the quiet stone streets of the wonderfully preserved Nagamachi Samurai district, where you can sit on a tatami and sip tea while admiring the gorgeous gardens of the Nomura residence. The most magical experience by far is exploring Kenroku-en, open at night and lit up with pink lanterns for hanami, cherry blossom viewing.

The cure for a night spent the chilled air and freezing rain lies back in the ryokan. A large stone bath, filled with hot water dispels the cold. But it is not just the bath, but the slow process of washing yourself first, tipping those buckets of hot water over your body to cleanse it before slowly descended into the heated pool, whereupon the aches and tension from a day on your feet slowly dissolves away. Then you lie down upon your futon, your nose close to straw of the tatami, and breathe in its scent as your drift into a warm sleep.

Despite making yearly trips to Japan, it is another five years before we stay in another ryokan. Whilst the experience of staying in a ryokan is unsurpassed, they are often inconveniently located away from transport and their traditions can be restrictive for the independent traveller who wants to explore late into the evening. In the intervening time we had also welcomed our child into the world, which lead to needing private bathroom facilities, not the shared baths of a ryokan.

March 2011 was also the month of the Tōhoku earthquake and tsunami with the resulting Fukushima Daichi nuclear reactor meltdown. As a result we changed our bookings to visit northern Japan and flew to the southern island of Kyushu instead.

In the intervening travels we had also discovered the joys of the onsen. Natural hot springs and ryokans are often connected, as Japanese will travel from far and wide for their reputed healing powers. Yufuin is a historically preserved town in Kyushu famous for its hot springs and its backdrop of the twin-peaked Yufu-dake.

The scenic Yufuin no Mori tourist train delivers us to Yufuin, where the tourist office books us into the reasonably priced Ryokan Hasuwa. The very friendly owner Madoka-san, who speaks excellent English, drives down to collect us and our luggage.

Ryokan Hasuwa sits by the railway line, great for train fans like me! However, what really makes it special compared with previous ryokan stays, are the two rotemburo, or outdoor baths. Bookable for families, and screened for privacy, one is a large wooden bath, the other a more naturalistic rock pool, beautifully lit by night. The pleasure of relaxing in a hot pool beneath the stars.

Many ryokans provide meals to guests, usually in their rooms. Others, like the Hasuwa, have dining room. A traditional kaiseki set, composed of multiple individual dishes, is both a pleasure and a curse of Japanese ryokan dining. In this case it is the former, a blend of western and Japanese dishes. Nabe stew cooked at the table, a salmon carpaccio in mint dressing, grilled salmon, pickles and rice.

The next morning one of the elderly cooks comes over to our son and makes him an origami samurai hat of newspaper, eliciting the smiles and giggles, the personal touch, that can make a ryokan stay so special.

Gujo Hachiman is one of Japan’s hidden gems. Nestled in the mountains at the confluence of the Nagara and Yoshida rivers, the town is overlooked by a authentically reconstructed wooden castle and is home to Japan’s replica food industry.

We chose the Ryokan Azumaya for its location conveniently near Gujo Hachiman station on the wonderful little Nagaragawa Line. It is a simple little ryokan with owners who speak little English, but both our stays were more than comfortable.

We delight in the kotatsu, a foot heater in a well beneath the low table, blankets covering our legs, warming us while we take tea. The room is decorated with beautiful pottery and scrolls hanging from the walls. At night we wash in the stone bath available to families, the hot water curing the mountain chill.

I visit the Azumaya twice, first with my family, the second with my mother. No food is served in the ryokan, but melt-in-your-mouth Hida beef can be found in the restaurants in town. In our exhaustion I purchase hot foods from a nearby kombini, the name for the convenience stores found all over Japan, and we eat while our legs are warmed by the kotatsu.

Gujo Hachiman’s town centre is a bit of a walk from the station, but across the road is a small café with decorative plants and flowers in its windows. One of the pleasures of Japan is a breakfast set. Thick slices of sweet toast, a boiled egg and a salad accompanied by a coffee or, in my case, a delicate porcelain cup of lemon tea. Then it is time to set out on the next leg of the journey.

Of all our ryokan experiences in Japan, this would have to be our most remarkable. Kinosaki Onsen is, as its name suggests, an onsen town. People come from all over Japan to bathe in its seven public bathhouses scattered throughout this historically preserved town.

The tourist office looks after the transport of our luggage, leaving us free to walk alongside the willow tree lined canal towards our accommodation.

We are greeted at the door by the very friendly Takayuki-san, who gives us a tour of the ryokan and shows us to our room. He then leads us to another room for the very important task of selecting a yukata. In Kinosaki Onsen guests stroll between baths dressed in their colourful yukata robes, reminding us not coincidentally of Jedi from Star Wars.

The task of choosing a yukata is disrupted by something else in the room. Toys. Lots of toys. Our son’s eyes were drawn to the bright blue plastic Plarail tracks and the trains that ride on them. This ryokan was a kid’s dream!

Although the ryokan has its own hot springs baths with views out to their manicured hillside gardens, we elect to don our yukata and join the others in exploring the town to try the public bathhouses. We return to take dinner in our room, attendants serving us dishes of local Tajimi beef, crab, soup, chawan mushi savoury custard, tempura and, finally, a dessert of green tea pudding with rice balls, yam and mandarin jelly, our stomachs filled until they can take no more.

At our son’s insistence, we let him play in the toy room until its 9 pm closing time. I go out again to wander the streets, to admire the new cherry blossoms under the pink lanterns. White lanterns illuminated the willows along the canal and the surrounding buildings. In an old fashioned ice cream parlour, still open this late at night, the sound of Joe Hisaishi’s music to Spirited Away just serves to make the scene even more magical than it is.

When I return, we all decided to head out again to visit one last bathhouse before we curl up on our futons laid out on the straw tatami, dreams merging with life.

We alight from the Resort Shirakami, a tourist train with live shamisen performances that runs along the incredibly scenic Gono Line, at Wespa Tsubakiyama, a psuedo-European resort with castle styled buildings. A shuttle takes us to the isolated Furofushi Onsen Hotel.

The lines between a hotel and a ryokan can sometimes be blurred. Many hotels have both tatami rooms where you sleep on a futon along with western style with standard hotel beds. The Furofushi Onsen Hotel is one of these, a health resort perched at the edge of the Japan sea, but our experience was that of a ryokan.

What makes this onsen special are the muddy iron open air hot mixed gender baths right on the seashore, surrounded by stone walls and rickety bamboo screens. There are indoor baths too, not particularly clean or inviting, but reputed to have great healing properties.

We use the rest of the day to explore the Oiwa Rock at nearby Fukaura and the exquisitely beautiful Juniko, the twelve lakes in the perhistoric Shirahama forests. After bathing in the seaside bath, we return to our room to watch the sun serenely sink beneath the sea.

Dinner, served in our room as we sit on the tatami, is the most elaborate of all our ryokan meals, perhaps our lives. Here we face the conundrum of the traditional kaiseki. Laid out on the table before us is thinly sliced sashimi, bowls of fish stew upon burners, cooked salmon, pork and pickles. But also seaweed noodles, whelks in their shells, a bowl of fish livers. An expectation that we will try the local apple flavoured sake. Some you need to grow up with to enjoy. Others are a matter of personal taste. There is the concern of giving offence, for all are delicacies and prepared so delicately. What is one to do?

It is my wife’s birthday and as a treat we are travelling to Takayama. This wonderfully preserved mountain town is famous for its history, it wooden carvings and the matsuri, a festival involving a parade of giant wooden floats. But what we are here for is Hida gyu, the local beef. Sadly, once you have tasted this perfectly marbled treat, served usually as thin slices or small cubes, no other steak will ever be as good.

Walking through the entrance of Hotakaso Yama no Iori, beneath the hanging nori and into their front courtyard, feels like stepping back into feudal Japan. Guest names hang from the signpost outside the entrance to the large lobby, where attentive staff are ready to offer assistance.

Takayama is popular with both local and foreign tourists. In the decade since our first visit to Takayama Japan’s popularity with foreigners has exploded and you cannot walk the streets without hearing accents from across the world.

We choose not to take dinner at the hotel, instead returning to our favourite Takayama restaurant, where we grill local beef and mountain vegetables over a gas stove at the centre of our table. Only a sprinkling of salt over the beef, a dip in the sauce for the vegetables, is required to bring out their flavour.

After bathing our feet in the river and stepping back in time at a Showa-era museum filled with old shop houses, a school room and old arcade and pachinko games, we return to the hotel with a strawberry and cream cake to celebrate the birthday. Candles and cake in a ryokan, followed by a hotel bath. What could be a better way to mark a new year of life?

I am on a quest to visit the compass points of the Japanese railway system. So far I have done the northern most station of Wakkanai and passed the most easterly point while travelling to Nemuro, both in Hokkaido. But now it is time to join the family in Honshu and spend some quality time together.

Japan’s railways will take you to some remarkably isolated destinations. We are in Unazuki Onsen in Japan’s Central Alps. The Kurobe Gorge railway was built to serve the giant hydroelectric scheme that is powered by the mighty Kurobe River. Though it continues to transport supplies and workers to the dams, the narrow gauge railway also carries tourists along the steep and scenic route.

Unfortunately for us, flooding has stopped the day’s operations and cut the length of tomorrow’s run by two-thirds. There is still much to see, with both the mountain gorge scenery and impressive manmade bridges and dams and this is an onsen town, with scorching public footbaths to relieve weary feet.

We have booked a tatami room in the Green Hotel, overlooking the river. Framed by the open paper shoji screens it is a beautiful sight. The quiet wooden corridors of the hotel remind me of the bathhouse from Spirited Away and indeed there are bathing facilities. We first try the indoor baths, but then step outside into the naturalistic setting and stone floor of the outdoor bath, savouring the delicious contrast between the heat of the water and the chill of the mountain air at night.

Here, away from the neon lights and noises of the cities, the magic of Japan lives on.

Hokkaido, the northernmost of the main islands of Japan, is a lonely and wild place, lacking the population and history of its southern neighbours. This was the domain of the Ainu, who have their own culture and traditions. We have been doing a circle around the island and, for the first time in Japan, hired a car for a day.

I had passed Kawayu Onsen on a train on my last trip to Japan, noting the strong stench of sulphur from Mount Io, and wanted to return. Yellow sulphur crystallises out of the boiling waters that flow out of the dormant volcano, the source of the tiny town’s onsens.

The Parkway Hotel itself has six baths, one mixed. We had initially hired the car to drive to the Shiretoko Peninsula, but a passing typhoon renders the day too wet, so we use it to explore the sights.

After dropping the other two off at the hotel, where they had the most delicious of dinners, I return the car north to Abashiri, driving in the night, wary of the deer we saw on the way down. I then catch the train back to Kawayu Onsen.

The station building features a statue of a bear and indeed I am warily looking out for any as I walk up the main street to the distant hotel in the lamplit darkness. The wind has died down and there is only the occasional spit of rain. The hooting of owls breaks the silence, while clouds of steam drift up from the drains where the waters of Mount Io flow and touch the cool night air.

It is truly magical and I just wish the one of the tiny cafes that line the streets were open for a hot tea or chocolate. Something to prolong this journey.

When I re-join the others at the hotel we head out to take our baths. First indoor, then outdoors under the night sky. Time stops, there is only the sensation of hot and cold.

Then, for the last time, we lay down on our futons and breathed in the scent of straw.