The pygmy raccoon (Procyon pygmaeus) of Cozumel Island, Mexico, is among the most endangered carnivores in the world, and causes of its decline are unclear. During 2002 and 2003, we sampled approximately 10% of the remaining population to survey exposure to viral and parasitic pathogens that may have contributed to population decline. We found evidence of exposure to infectious canine hepatitis, canine distemper, feline panleukopenia virus, and Toxoplasma gondii. The latter is suggestive of spillover from domestic cats, which have only recently been introduced to the island. Additional parasites identified include Eimeria nutalli, Placoconus lotoris, Capillaria procyonis, Physaloptera sp., a mite in the family Listrophoridae, and a trematode in the family Heterophyidae. Several of these are typical of the parasite community of the common raccoon (Procyon lotor).