Black mold (BM), caused by Aspergillus niger Tiegh., is a common onion (Allium cepa L.) postharvest disease under hot and humid storage conditions. This study aimed to develop a BM screening protocol, to evaluate onion cultivars for resistance. The effects of pathogen isolate, inoculum density, incubation temperature, and inoculation method on severity of BM were investigated in designing the screening protocol. Variation in virulence was observed and two highly virulent subcultures, An4-2 and An39-3, were selected for study. Disease severity, both in lesion size and sporulation degree, increased with higher inoculum densities and incubation temperatures. In contrast, small lesions and no sporulation were observed when onion scales were inoculated with 1 × 104 spores/mL or incubated at temperatures lower than 20 °C. Inoculation of onion scales or entire bulbs were compared and scale inoculation correlated better with BM incidence in storage. The procedure for BM screening protocol included: wound inoculation of onion slices with 40 μL inoculum suspension of 1 × 105 spores/mL, incubation at 25 °C with 12 hour photoperiod, and rating lesion diameter and sporulation 4 days after inoculation. Using this screening protocol, 42 onion cultivars were evaluated and cultivars with better storability such as `Red Pinoy', `Serrana', `Dehydrator No.3', and `Moonlight' were tolerant to A. niger. These cultivars showed small lesions and no sporulation during screening. On the other hand, cultivars with poor storability like `Texas Early Grano 502', `Granex 429', and `Explorer' exhibited larger lesions with profuse sporulation. Lesion diameter caused by the scale inoculation correlated significantly with bulb storage loss (r = 0.51, P < 0.01) as well as with bulb dry matter (r = -0.48, P < 0.01) and total soluble solids (r = - 0.51, P < 0.01). The screening protocol and tolerant materials are now successfully used in the Asian Vegetable Research and Development Center onion breeding program for resistance to black mold.