Having Tattoos in Japan

Being a tattooed women I wondered how my ink would impact my Japanese experience. From what I've gathered Japan has had a long history of disliking tattoos and the stigma is still present today. Rarely, will you see a Japanese citizen with tattoos, and the few that do can be seen as outsiders in Japan. The stigma of tattoos in Japan may worry a few foreigners about visiting, but it's actually less of a problem than you think. Here are a few tips on visiting Japan with ink.
Why Do the Japanese Not Like Tattoos?
We'll start off with a little history lesson. The stigma of tattoos dates back to about 720 AD where tattoos were meant to punish criminals. Criminals that committed serious crimes would be marked with a tattoo that symbolized their offenses. These people were shunned by their family and ostracized by their community. When the practice of marking criminals ended Japan outlawed tattooing all together.

During the Edo period tattoos were adopted by outlaws and gangs such as the Yakuza. Because of the pain and permanent nature of tattoos the Yakuza viewed them as a symbol of courage and loyalty.
History Source: http://www.vanishingtattoo.com/tattoo_museum/chinese_japanese_tattoos.html

The history associated with tattoos is primarily why the Japanese dislike them, but there are a few other smaller reasons.
Some Japanese people believe that tattoos make your skin dirty and impure. This belief is primarily held by people who are religious, but even those who aren't religious in Japan agree.  Tattoos are also seen as disrespectful to your parents and ancestors who gave you your body, destroying it with tattoos is highly taboo.
What Can't You Do With Tattoos?

There are some places you can't go if you're covered with ink.  You've probably heard that you can't enter Onsen if you have tattoos, this is mostly true. Some facilities will allow you and some won't, usually they'll have signs up stating if tattoos are allowed or not. I've had an English teacher who had a full sleeve and was able to enter an Onsen because he covered them with tape, but it really depends on the owner of the Onsen.

Public pools and some gyms are other places you can't go if you have tattoos. The reason for this is because not everyone approves of tattoos and will feel uncomfortable being around you with so little clothes on. You can probably get away with working out in a gym if you have a small tattoo that can be covered up, sleeves however, maybe a little bit more difficult to cover up.
Covering Tattoos
There are ways of covering tattoos if you don't want unwelcome stares while visiting Japan. If you have a couple small tattoos on your arm than covering up tattoos with foundation is no problem, but it's a bit complicated if you have sleeves. There a couple products out there that are specific to covering up tattoos, a quick google search will give you many different options raging from 6$ to 50$. The only downside to this is that you can't go into the water with makeup or it will wash off and you could get in trouble.
Changing Attitudes
Over the years the attitudes towards tattoos have been slowly shifting. With the constant influence of the west and more foreigners coming into the country with tattoos younger generations are starting to loosen up. While you may get disapproving stares from older Japanese citizens younger people will be more fascinated rather than weirded out by your art.  
Depending on where you go in Japan will determine if it's ok to show your tattoos or not, it's usually best to be cautious. Always carry some cover up foundation with you just in case it starts to fade during the day, and enjoy your time in Japan!