Polymerase chain reaction (PCR) was applied to confirm the diagnosis of brucellosis and to study its clearance in response to the standard treatment regimen with doxycycline and rifampin at hospitals in Callao and Lima, Peru. The PCR confirmed the diagnosis in 23 (91.7%) patients with brucellosis including 12 culture-confirmed cases. For patients treated at the hospital in Callao, PCR was positive for all samples collected during and at the conclusion of treatment and for 76.9% of follow-up samples collected on average 15.9 weeks after completion of treatment. For patients treated at the hospital in Lima, PCR tests were positive for 81.8% of samples collected during treatment, for 33.3% of samples collected at the conclusion of treatment, and for ≥ 50% of samples collected at first, second, and third post-treatment follow-up. Thus, Brucella DNA may persist in the serum weeks to months after completion of the standard treatment regimen.