BACKGROUND: Extrapulmonary infection or dissemination of Pneumocystis carinii (PC) is rare, but under certain conditions the parasite can spread via the bloodstream or lymphatic vessels. Systemic pneumocystosis most often involves the lymph nodes, stomach, spleen, liver, skin, pancreas, choroid and eye. Isolated lesions containing PC have also been identified in the thyroid. CASE: A 41-year-old, homosexual male infected with the human immunodeficiency virus (HIV) developed a PC infection in the thyroid gland. The patient had had thrush and anal herpes since being diagnosed as HIV positive in 1984. In 1992 the patient developed a mass in the area of the right lobe of the thyroid gland. Smears from fine needle aspiration cytology of the thyroid mass revealed epithelioid cells. However, a cell block revealed numerous PC organisms on Gomori mithenamine-silver stain; that finding was confirmed by an excisional biopsy. The patient had not previously been diagnosed with PC pneumonia. CONCLUSION: Our case of thyroid involvement with PC expands the clinical spectrum of extrapulmonary pneumocystosis in patients with the acquired immunodeficiency syndrome. We believe that in these patients the incidence of Pneumocystis thyroiditis will continue to rise and be reported.