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 g kg-1 (mean = 0.4 g kg-1) and from <0.05 to 3.5 g 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 g kg-1 (mean = 0.1 g kg-1). Fumonisin B1 was found in 32% of the white yam samples (<0.5 (LOD) to 91 g kg-1; mean = 5 g kg-1) and in 5% of water yam samples (<LOD to 2 g 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.