The natural occurrence of aflatoxins (AFs) and fumonisins (FBs) in yam flour samples (n = 100) obtained in south-western Nigeria was evaluated. AFs were determined by HPLC with fluorescence detection and FBs by HPLC coupled with mass spectrometry. Aflatoxin B1 (AFB1) and aflatoxin G1 (AFG1) were found in 57% and 21% of flours from white yam with concentrations ranging from <0.02 (limit of detection, LOD) to 3.2 μg kg−1 (mean = 0.4 μg kg−1) and from <0.05 to 3.5 μg kg−1, respectively. AFB1 was the only aflatoxin detected in samples from water yam, contaminating 32% of the samples with values ranging from <LOD to 0.6 μg kg−1 (mean = 0.1 μg kg−1). Fumonisin B1 was found in 32% of the white yam samples (<0.5 (LOD) to 91 μg kg−1; mean = 5 μg kg−1) and in 5% of water yam samples (<LOD to 2 μg kg−1). AFs and FBs were significantly higher (P < 0.05) in white yam flours compared to water yam flours. Preparation of amala from naturally-contaminated yam flour resulted in reduction of AFB1 and AFG1 by 44% and 51% respectively. From this study, only 7% of the samples contained AFs above the European standard limits for cereals intended for direct human consumption, while all the FBs-positive samples were well below the limits. The occurrence of ochratoxin A, zearalenone and deoxynivalenol was also evaluated in 20 samples; these mycotoxins were never detected.