I see from other sites that some of the bars in Shinjuku Golden Gai only welcome local Japanese, so how do I know if they don't welcome foreigners?
Should I pick those bar with cover chanrge to play safe?
Or any other hints?
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One of the best ways would be to read through the Tripadvisor reviews on Shinjuku Golden Gai. There are many experiences there referencing specific bars and places, most of them very positive. You can find the places to avoid by looking for the bad reviews!
As a former Tokyo resident, I think the open-door/closed-door suggestion is a bit too conservative - it will probably ensure you don't end up anywhere you are not welcome, but also may mean you miss out on some great places and experiences. The Japanese are typically accepting and polite. I think a better rule of thumb is whether there is any English signage.
If you have a companion or friend with some Japanese ability, or you are comfortable being in a context even where no English is spoken, then I wouldn't even worry about that, but would pick anywhere with a few excess empty seats, ie you are less likely to be taking the place of a local. Be aware that you do risk being treated gruffly if you take this approach and end up somewhere that doesn't want you there, but often they'll come around if you fit into the place well enough.
By the way, if you are interested in Shinjuku Golden Gai, you will also very likely enjoy nonbei yokocho in Shibuya. Check out Tight, a micro-bar with a friendly owner.
This is from my experience, but you don't always have to pay cover. A lot of places will offer different specials, one such place I went to had "Say hello to the bartender in your language" or "No cover for people visiting for the first time" they were really nice places. Some of the places that had a cover had people talking to us in english and welcoming us in, since they are small friendly places.
Also, some places may be unfriendly to foreigners, but every place I went to they were friendly, as long as you kept buying drinks (Some of the smaller places can and will ask you to leave if you stay too long with an empty glass)
My own experience is that they are mostly very welcoming to foreigners. We were six (Norwegian) guys walking around the narrow streets, basically just sticking our heads in the doors asking if there was room for us (hand gestures and an asking expression on your face, mostly). Most of the places we tried had some form of english signage outside. The only rejections we got (as far as I remember) was the places that could not physically fit six more people (which counts out about half of the bars).
Would do the same again. Just ask if it's OK to come in.
Some of them even state things like "Foreigners welcome!" in more or less clumsy engrish on their signs.
Answer is simple.It's up to you.I mean it depend on your attitude.Almost bar is Welcome Foreigner,try best,even can't speek Engish,But some are give up to trying.Because almost Foreigner never try to understand this area's history,calture,and why this area still alive durring over 50years.After 1945,this town create great artist,filmmaker,noverist,musician,also now.so many regular costomer talk about calture and art speek gentley, smart,so inteligens.But now many foreigner know this town,comes many person everynights,10peaple grup comin'only 7seets bar,talk clazy loud,scream and shout, show their own iphone and insist [Play,this song!].Only 1beer order but stay 2hours. at last try to discount a check and can't understand cover charge[and why bar need it]. how does it feel? 1000chinese come to your Favarit bar, They shout so loud in Chinese language,and speak only with them.Now GoldenGai is in for trouble is absolutry same.Incude me,many regular customer leave this town,So many bars deside to change not so friendry for foreigner style.They tried accept foreigner,during many years , but Almost foreigner are no understand this town's rules and manners. so bars are disapoint this situation. In conciusion, If you understand the fact as I write,have god sense,everyone welcome.But doing like a high school rude kid,you will kick'n out.And don't forget speak Japanese at least when you order drink.