This study was undertaken to determine the value of incorporating fluorescence into cytopathological evaluation of lymph node fine-needle aspiration (FNA) specimens suspected of harboring mycobacterial species. The study population consisted of 1,044 HIV-positive and -negative patients referred for FNA to the cytopathology unit of a South African medical school located in a very high HIV prevalence region. Each aspirate was assessed on routine Papanicolaou-stained slides for morphologic characteristics of mycobacterial infection. The same glass slides were then viewed under fluorescent microscopy to determine the presence or absence of mycobacterial autofluorescence. Using multivariate analysis, results of both cytology and fluorescence were compared with mycobacterial culture as the final arbiter of the presence of organisms. In this large clinical study, compared with culture, cytomorphology showed sensitivity of 84.9%, but low specificity of only 50.9%. Fluorescence demonstrated lower sensitivity of 65.9%, but improved specificity of 73.0%. Taken together, positivity of both cytology and fluorescence improved specificity to 81.8%. Fluorescent microscopy is rapid, inexpensive, and cost-effective; neither radioactive materials nor further staining are required. It is felt that this methodology would be of diagnostic benefit if used on morphologically suspicious samples in areas with a high prevalence of HIV and mycobacterial infections. Appropriate therapy could be commenced within hours of FNA, with reduction in the current number of patients lost to follow-up while awaiting results of culture. The technique is readily extended to other FNA types such as deep organ aspirates. Autofluorescence of organisms specifically requires usage of Papanicolaou staining; the technique cannot be used in histopathologic specimens stained with hematoxylin-eosin.