An emergence of drug-resistant tuberculosis (DR-TB) in settings affected by human immunodeficiency virus (HIV) and tuberculosis (TB) has been observed. We investigated the prevalence of DR-TB in P1041, a multicentered, randomised, double-blind trial which compared the administration of isoniazid (INH) to placebo, in HIV-exposed, non-infected and -infected African infants in the absence of any documented TB exposure. The prevalence of multidrug-resistant TB (MDR-TB) was 22.2% (95%CI 8.5-45.8) and INH monoresistance 5.6% (95%CI 0.1-27.6) among culture-confirmed cases, with all MDR-TB occurring in a single site. There was no association between INH treatment or placebo group, or between HIV infection status, and DR-TB prevalence. There was a high prevalence of DR-TB among HIV-exposed and -infected children. Surveillance of DR-TB among children in high-burden TB-HIV settings should be routine.