Excessive weight loss due to protein calorie malnutrition (PCM) is a significant problem in Nigerian children. This syndrome may be difficult to differentiate from the wasting disease caused by human immunodeficiency virus type 1 (HIV-1) infection. We studied 70 children admitted to the Baptist Medical Center in Ogbomosho, Nigeria in 1990 with PCM for prevalence of antibodies to HIV-1 and HIV-2. The cohort was from low-risk mothers and had a median age of 25 months (range, 4 months–9 years) with a weight deficit of at least 20% of the theoretical weight for age. Two sera were positive for anti-HIV-1 by both ELISA and Western blot (WB). A high prevalence of samples negative for HIV-1 antibody by ELISA were repeatedly reactive (11%, 8/70) or indeterminate (46%. 32/70) by WB. None of the sera was positive for antibody to HIV-2. There was no correlation of ELISA positivity or extent of WB banding with successful recovery from malnutrition. These results indicate a relatively low but significant prevalence of HIV-1 infection in Nigerian children with PCM. The high prevalence of indeterminate reactions in WB assays for HIV-1 suggests that other procedures may be necessary for confirmatory diagnosis of HIY-1 infection in this African population.