In this study, natural mycoflora of 30 raw and 50 roasted hazelnut, 20 hazelnut paste and 50 inner membrane samples and their total aflatoxin contents were determined. In mycological isolations, 1.8-2.56% of Aspergillus flavus and 42.7-65.44% of A. niger were determined in the raw hazelnut samples. A. flavus (2.2-12.2%) and A. niger (33.3-74.5%) were also detected in roasted hazelnut, while the percentages of these microorganisms in hazelnut paste samples were 0-13.1% and 43.5-100.0%, respectively. The ratio of A. flavus and A. niger in inner membranes was found to be 2.6-16.2% and 44.6-89.4%, respectively. Aflatoxin analysis showed that the levels of aflatoxin were 2.11–10.03 ppb in raw hazelnut, 0.1–4.04 ppb in roasted hazelnut, 0.2-6.02 ppb in hazelnut paste samples and 0.7-38.2 ppb in inner membrane samples. While only one of the raw hazelnut, roasted hazelnut and hazelnut paste samples had toxin above the legal limit, 100% of the inner membrane samples showed different levels of aflatoxin contamination. Since there is no limitation in the Turkish Food Codex on hazelnut inner membrane, the amount of aflatoxin, which is higher than 10 ppb in 25 of the samples, was considered to be high contamination. Kruskal Wallis and Mann Whitney U analyses were used for statistical evaluation of the samples. There was a significant difference in aflatoxin formation and moisture content between the samples in different groups (p <0.05).