Anterior chamber aspiration and vitreous aspiration were evaluated as diagnostic procedures for establishing a specific microbiological diagnosis in the rabbit model of hematogenous Candida endophthalmitis. Vitreous aspiration was the most successful procedure, confirming the diagnosis of hematogenous Candida endophthalmitis in 62% of eyes with documented intraocular infection. When animals with only the most severe clinical endophthalmitis were considered, vitreous aspiration confirmed the diagnosis in 89% of eyes evaluated. Vitreous aspiration correlated well with the extent of clinical endophthalmitis, as well as with postmortem, whole-vitreous cultures. Gram staining of the aspirate was additive to culture results in confirming the diagnosis. Anterior chamber aspiration was positive in only 1 of 58 eyes evaluated (1.7%). Additionally, muscle biospy was evaluated in this study as a tool for establishing a microbiological diagnosis in the rabbit model of disseminated candidiasis. Only 2 of 131 biospy specimens contained detectable Candida. Although vitreous aspiration may be associated with ocular complications, in certain clinical settings this procedure may be valuable in establishing the definitive microbiological diagnosis of hematogenous Candida endophthalmitis.