The risk of Mycobacterium bovis bloodstream infection (BSI) in bacille Calmette-Guérin (BCG)-vaccinated children with human immunodeficiency virus (HIV) infection remains uncharacterized. We studied pediatric inpatients during the 1998 dry season in Malawi. After a detailed clinical evaluation, blood was drawn for culture and HIV testing. Of 229 children, 128 (56%) were male, 35 (15.3%) had BSI, and 30% of children aged >1.5 years (median, 2.7 years; range, 1 month-13 years) had HIV infection. The predominant pathogen was non-typhi Salmonella; neither Mycobacterium tuberculosis nor M. bovis was isolated. A diagnosis of malnutrition or sepsis was predictive of BSI; malnutrition alone correlated with both death and BSI. The bloodstream dissemination of M. tuberculosis and M. bovis BCG is uncommon in HIV-infected children vaccinated with BCG. Correlates such as malnutrition or sepsis can provide algorithms for identifying children who need observation or empirical antimicrobial therapy for BSI in the absence of appropriate laboratory testing.