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Abstract Background Cryptococcal prostatitis is a rare clinical disease and has never been reported in China. Case presentation We report on a male HIV-infected patient with pulmonary and prostate cryptococcosis that was misdiagnosed (as tuberculosis) and delayed diagnosed. Although the patients accepted anti-fungal treatment and anti-retroviral treatment finally, the physician’s mistakes reflect the rarity of this condition in China. Conclusion Cryptococcal prostatitis is a rare disease that unusually presents in immunodeficient patients. Physicians should have a heightened awareness of this particular infection in the immunodeficient population.