Enterocytozoon bieneusi is a microsporidian that causes a severe, debilitating, chronic diarrhea in some patients with the acquired immunodeficiency syndrome. Specific diagnosis of E. bieneusi currently requires an invasive biopsy procedure and time-consuming preparation of specimens for electron microscopy. Our attempts to establish an in vitro culture system using mammalian cell cultures inoculated with duodenal aspirates, biopsy, or both, from 2 infected patients resulted in inadvertent coculture of an adenovirus and E. bieneusi. The adenovirus-infected cells deceptively appeared to contain spores of microsporidia based on light microscopic examination. Transmission electron microscopy revealed only a few microsporidia, but numerous cells infected with an adenovirus that was subsequently identified as adenovirus type 8. We believe that adenovirus infections prevented the cultured cells from supporting the proliferation of E. bieneusi and ultimately destroyed the cell cultures.