This study was carried out to assess the seed-borne fungi of onion in Burkina Faso. Eighteen onion seed samples were collected from local farmers and wholesalers of vegetable seeds in the country and were investigated for fungi. The investigation was done using the “blotter method” on dry seeds and on seedlings. Fungal contamination was detected in all 18 tested samples. Seventeen fungal species belonging to 11 fungal genera were identified in the seed samples: Aspergillus was detected in 17 samples, Fusarium and Rhizopus in 15 samples, Cladosporium in 14 samples and Penicillium in 13 samples. Aspergillus niger and Fusarium oxysporum, known to be the causal agents of black mould and basal rot diseases, were detected in 17 and 11 samples, respectively, by seed analysis and in 10 and 9 samples, respectively, by seedling analysis. The infection rates by the fungal species varied from 0 to 90.3% for A. niger and from 0 to 13.5% for F. oxysporum. Alternaria porri, the causal agent of purple blotch disease was recorded lowly on two seed samples at infection rates of 0,5 and 1%. Exotic seed samples showed better health quality compared to local seed samples. These results indicated that the seeds locally produced by farmers in Burkina Faso are for low health quality and needs strong treatments before use to avoid diseases appearance in fields.