Usagi Yojimbo is currently published by Dark Horse Comics in TPB form. In the past it has also been published by Mirage Studios and Fantagraphics.

A few notes for people interested in Teenage Mutant Ninja Turtles cross-overs, "Usagi Yojimbo Book Three", published by Fantagraphics contains an epilogue where Leonardo is transported back in time. Leonardo is attacked by outlaws on the same road where Usagi is attacked by ninjas. The two battles merge, and they are the last left standing. They both assume the other is an enemy and attack. They charge each other, and Leonardo is transported back to his own time just before they can actually strike.

Another cross-over occurs in "Usagi Yojimbo, Shades of Green" published by Mirage Studios (Which is also contained in the Dark Horse Comics volume "Usagi Yojimbo, Shades of Death"), where a rat named Kakera transforms 4 turtles into the Teenage Mutant Ninja Turtles to aid Usagi and his friend Gen.