Shadow Dancer does not really have any regional differences -cartridge wise no matter what regional variant of the game you have, you'll have the same as everyone else. But the game's story is another matter. In the Japanese version of Shadow Dancer, you play as Hayate Musashi, Joe's son. The game manual references the original Shinobi, stating it took place in 1977, and that this game takes place in 1997. For the non-Japanese versions, the story was changed so you are playing as Joe Musashi instead, and the game manual does not mention the original Shinobi. Why SEGA of America decided to change this is a mystery.

The only other difference is that some of the bosses have different names in the Japanese version. Again, this is not shown in the game itself, but in the manuals or on the boxes. For example, the last boss of the game isn't named in the Japanese version, but was given the name of Sauros in America and Europe.

One oddity with the Japanese version of Shadow Dancer is that the intro is still in English, even if you are playing a Japanese cartridge on a Japanese machine. The same thing happens in the Japanese version of the previous game.