Cryptosporidium infection was confirmed by fecal examination for the first time in pet rabbits in a wholesale store located in Kanagawa Prefecture, Japan. Fecal samples were obtained postmortem from juvenile rabbits (n=66), which had died after developing diarrhea. Feces from healthy rabbits (n=30) were also collected and examined as controls. Two types of Cryptosporidium oocysts distinctive in size and shape were found (Type A and B). Types A and B oocysts were detected from 16.7% and 13.6% of the diarrheic, and 3.3% and 0% of the normal feces, respectively. Since Cryptosporidium oocysts were detected at a higher rate in the diarrheic rabbits than in the healthy rabbits, special caution should be taken when handling a pet rabbit presenting with diarrhea.