Seed health testing of fifteen soybean cultivars obtained from five locations in the Guinea Savannah agro-ecology of Nigeria was carried out using two main seed health testing methods described by the International Seed Testing Association (ISTA); the standard blotter and two variants of agar plate incubation method (Potato Dextrose Agar and Czapeck Dox Agar plate methods) to determine the seed infection by fungi. Seed component plating was also carried out to determine the most active site of infection of the seeds by the fungi. Five fungal species were isolated from the cultivars tested. The percentage of seeds infected with Fusarium sp.andPenicillium sp. was significantly different (p<0.05) among the cultivars, with the highest value standing at 15.20 percent of Fusarium sp. and 8.54 percent of Penicillium sp. in cultivars MSJ and FSSBu, respectively. The difference in the methods of isolation was also significant (p<0.05) and the agar (PDA) plate method was the most efficient in the isolation of Aspergillus sp., Penicillium sp.andPhomopsis sp. The efficiency of the other methods of isolation however varied for the different organisms. The cotyledon was observed to be the most active site of infection with thirteen of the fifteen tested cultivars showing 40–100% of infection of the cotyledons. The need for soybean seed health testing before their distribution to farmers is made manifest in this study.