BACKGROUND: Kaposi's sarcoma (KS) is caused by Kaposi's sarcoma associated herpesvirus (KSHV/HHV-8), the eighth Herpesvirus found to infect humans. The molecular epidemiology of KSHV is related closely to ethnicity and geographical location of studied populations. There is little epidemiological and molecular information about KSHV strains circulating in Brazil. OBJECTIVES: To characterize KSHV strains isolated from AIDS patients with Kaposi's sarcoma (AIDS-KS) in Sao Paulo, Brazil, and to examine associations between KSHV subtypes, ethnicity and HIV risk categories. METHODS: AIDS-KS patients were recruited consecutively at the largest AIDS reference hospital in Sao Paulo. Fragments (420 bp) of the VR1 and VR2 regions of KSHV open reading frame (ORF) K1 were amplified by nested PCR and sequenced directly. RESULTS: We analysed 37 samples from 33 patients, and found subtypes A-C in 48%, 21% and 30% of patients respectively, including two patients infected with subtype A5, a first report from Brazil. Sexual orientation was associated with subtype: 12/14 (86%) patients with subtype A were male homo/bisexual, compared with 3/8 (38%) among patients infected with subtype C (P = 0.05). A higher proportion of male patients with subtype C were of Caucasian origin (7/8 (87%)), compared with 7/16 (44%) among male patients with subtype A (P = 0.08). CONCLUSIONS: This first detailed report of KSHV subtypes among AIDS-KS patients in Brazil reports the first isolation of KSHV subtype A5 in this country, and suggests KSHV strain transmission between different ethnic groups, and association of specific strains with sexual orientation.