Aflatoxin (AF) contamination of food products is still a major health issue globally. Prior studies suggest that exposure to AFs during pregnancy has harmful fetal outcomes. This preliminary study was designed to assess serum AFB1 levels in neonatal jaundice (NNJ) secondary to glucose-6-phosphate dehydrogenase (G6PD) deficiency. Twenty-four full-term neonates with haemolytic jaundice secondary to G6PD deficiency were enrolled in the study. Erythrocyte G6PD status was assessed calorimetrically, and serum aflatoxin B1 (AFB1) concentrations were measured by high-performance liquid chromatography. The results revealed that AFB1 was detected in 58% (14/24) of the studied newborns while detected in 75% (18/24) of their mothers. AFB1 positive cases had a highly significantly lower birthweight and G6PD activity (P = 0.001, each). Birthweight (r = − 0.574, P = 0.032) and G6PD activity (r = − 0.585, P = 0.028) negatively correlated with serum AFB1 levels while serum alanine aminotransferase activity positively correlated with serum AFB1 levels (r = 0.536, P = 0.048). Maternal AFB1 exposure is associated with adverse birth outcomes as verified by the low birthweight and the evident decline in the activity of G6PD enzyme with the resultant haemolytic