Fifteen Swiss-Webster mice (Mus musculus) and eight cotton rats (Sigmodon hispidus) were inoculated orally with Caryospora bigenetica oocysts. Feces from these animals were collected from 0 to 180 days postinoculation (DPI) and examined for endogenously-produced oocysts using Nomarski microscopy. Oocysts were recovered from mouse feces at 0, 1, 2, 3, 5, 7, 8, 10, and 14 DPI, and from cotton rat feces at 1, 2, and 9 DPI. The recovered oocysts were determined to be from the original inocula due to the presence of thick walls, polar granules, and Stieda and substieda bodies. All animals exhibited clinical signs at 8 DPI. Developmental stages of C. bigenetica were identified in various tissues of seven cotton rats found dead at 9, 10, 11, 12, and 13 DPI. Caryocysts were found in muzzle, tongue, footpad, scrotum, and rectum of mice and cotton rats at 30 DPI. Fecal samples collected from mice on 0, 8, 10, 12, 14, 16, and 18 DPI, and from cotton rats on 0, 9, 11, 13, 15, and 17 DPI were injected subcutaneously into 13 mice. Of the 13 mice, a Caryospora infection was observed only in the mouse inoculated with 0 DPI mouse feces. We propose that endogenously-produced C. bigenetica oocysts are not fecally-transmitted by Swiss-Webster mice or cotton rats.