Species of Aspergillus produce a class of mycotoxins known as aflatoxins. For both humans and animals, aflatoxins are poisonous and cancer-causing agents. A potential threat to consumer health, therefore, exists when aflatoxins are found in food. In market meat, particularly in chicken and duck, there have been few reports of aflatoxins residues. As a key source of protein, poultry products are one of the foods that are consumed widely in Egypt. So, the goal of this study was to use HPLC for measuring the total aflatoxins (AF) and aflatoxin B1, B2, G1 and G2 levels in chicken and duck flesh and liver. A total of 100 samples were collected throughout the study period, including 50 samples of chicken meat (25 muscles, 25 liver), and 50 samples of duck meat (25 muscles, 25 liver). Findings showed that the samples investigated varied significantly (p values). The highest total aflatoxin residues were detected in the liver in both chicken and duck (6.61± 1.51, 6.15±1.75 ppb respectively), while in the muscles it was lower (0.07±0.005, 0.071±0.03 ppb respectively). Moreover, the amount of aflatoxin residue found was highest in duck liver (6.15±1.75 ppb) 80% from total examined samples, whereas it was significantly lower in chicken (Liver, muscles) and duck muscles. The liver of the examined chicken and duck samples showed a significant differential variation (p values), however the muscle variation was statistically negligible. The presence of contamination in every sample is a health hazard, and it appears that more research is needed.