Bartonella henselae causes severe disease in immunocompromised individuals. B. henselae was isolated from 12 human immunodeficiency virus (HIV)-infected individuals with bacillary angiomatosis and/or peliosis hepatis and from their 15 cat contacts. Specific associations between the 2 B. henselae genotypes, individual pulsed-field gel electrophoresis (PFGE) patterns, and different clinical syndromes and pathogenicity were investigated. The role of cat contacts as the source of human infection was also examined. Three of the 4 patients with B. henselae genotype I infection, but none of the 8 patients with genotype II infection, had hepatosplenic vascular proliferative lesions (P=.018). Four of 5 human-cat pairs had closely-related PFGE patterns and concordant results by 16S rDNA typing, which strongly suggests that human infection was caused by the cat contact. These results corroborate the major role of cats in the transmission of B. henselae to humans and suggest that B. henselae genotypes may induce different pathological features in HIV-infected patients.