Bartonella infection can be difficult to diagnose, especially when it manifests as bacteremia, which is usually accompanied by nonspecific symptoms, such as fever. Therefore, we hypothesized that Bartonella infection represents an underrecognized cause of febrile illness. To determine the prevalence of Bartonella infection among patients presenting with fever, we evaluated 382 patients in San Francisco. Overall, 68 patients (18%) had evidence of Bartonella infection detected by culture, indirect fluorescent antibody testing, or polymerase chain reaction (PCR). Twelve patients (3%) had either Bartonella henselae or Bartonella quintana isolated from specimens of blood, tissue, or both or had DNA detected in tissue; all 12 had concomitant human immunodeficiency virus (HIV) infection. Bartonella antibodies were detected in 17% of febrile patients, including 75% of culture-positive or PCR-positive patients. In a nested, matched case-control study aimed at identifying clinical features of febrile illness associated with Bartonella infection, only bacillary angiomatosis and elevated alkaline phosphatase levels were associated with Bartonella infection (P< or =.03 for both). The prevalence of Bartonella infection among patients with late-stage HIV infection and unexplained fever is much greater than has previously been documented.