The company, which began in Oakland, California in 2002, hopes its early popularity is more than a passing fad. Japan's consumer culture is littered with manias for Western food imports: pancakes, popcorn, doughnuts, even Taco Bell.
Success in Japan is important for Blue Bottle, which operates 17 cafes in the San Francisco Bay area, New York and Los Angeles. Japan is its first foray outside of the U.S. Blue Bottle raised nearly $26 million last year to invest in expansion, including financing from Silicon Valley executives, setting the stage for a test of whether an artsy gourmet coffee chain can go big.
Founder James Freeman, a musician, was inspired by Japan's old-style "kissaten" coffee-shops: tiny dimly-lit establishments, with good music and a barista behind a wooden counter. Think places for quiet serious thinking and real drip coffee, not sweet, frivolous drinks.
"We care about every part of the coffee. We call it from seed to cup," said Saki Igawa, the business operations manager for Blue Bottle in Japan.
Attention to detail that dovetails with aspects of Japanese culture accounts for part of the coffee chain's early popularity. The spread of Starbucks internationally, which has created a cookie-cutter coffee culture that some people want to trade up from, is another factor. Blue Bottle is also benefiting from the image problems in Japan of fast food chains and highly processed foods.
"It's a new era in eating out," said food industry consultant Jotaro Fujii who contends that Blue Bottle's arrival and the decline of McDonald's in Japan is part of a bigger trend of consumer interest in the safety and quality of the entire food supply chain.
McDonald's is suffering declining popularity in Japan, a problem exacerbated after plastic pieces, and even a tooth, was found in its food last year, setting off outrage among consumers.
Upscale burger chain Shake Shack, which started as a hot dog stand in New York, is expected to arrive in Japan soon, said Fujii.
Such chains, including Blue Bottle, are likely to aim for 50 or at most 100 outlets in Japan, not the thousands that fast-food eateries, such as McDonald's, has achieved here, he said.
Instead, they will focus on fortifying a brand image, which can lead to other kinds of lucrative businesses.
Although the prevalent image of Japan might be tea, it has long had plenty of affection for coffee.
Starbucks has been a hit since arriving in 1995. It now has more than 1,000 shops in Japan. Not a single prefecture (state) is without a Starbucks with one opening in holdout Tottori Prefecture this month — not surprisingly, welcomed with long lines.
Even convenience stores are serving freshly brewed coffee. Japan also invented "manga-kissa," or a cafe-cum-library, where you can curl up with a comic book and sip on coffee for hours.
Such newcomers have hammered the once omnipresent kissaten. Their numbers have dropped by half from the 1980s, or to 77,000 in 2009, according to a Japanese government study.
But Blue Bottle's popularity is part of a rediscovery of cafes serving carefully prepared, quality coffee, a trend already long evident in the U.S.
Blue Bottle's first Japan shop, which has a roaster, is in Kiyosumi, an older part of Tokyo, chosen because it reminded Freeman, the founder, of Oakland. It opened in February. The second shop, in a backstreet of Tokyo's fashionable Omotesando, opened in March.
A third, likely opening later this year in Tokyo's Daikanyama shopping area, will feature a menu that reflects Blue Bottle's recent acquisition of San Francisco-based Tartine Bakery, which serves croissants, sandwiches and pastries.
Blends such as "Giant Steps," combining African and Indonesian-grown beans for a chocolate taste, sell for 450 yen ($3.75) a cup. A latte costs 520 yen ($4.30).
On a recent day, the Blue Bottle shop in Kiyosumi, Tokyo, was filled with sunlight pouring through huge windows, the hum of a giant roaster, the fragrant aroma of fresh coffee and a crowd of people.
Takuya Nakagawa, a 39-year-old hairdresser, who came all the way from rural Toyama Prefecture (state), was impressed with the coffee's taste and the store's stylish stark decor. He bought granola and coffee beans as souvenir gifts.
"I just love the taste," he said. "This kind of place doesn't exist in Toyama."
True to its inspiration, Blue Bottle is learning from Japan, said Andrew Smith, 29, of San Francisco, a barista and one of three Americans who came to work for the chain in Japan.
"People here have different ways of conceptualizing about coffee so they taste things differently," Smith said.
"They are looking for different kinds of things in coffee. And that is a fun way to learn how everyone in the world perceives coffee differently."
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