Seedling diseases are one of the major production problems for soybean. The primary control of soybean seedling diseases is by fungicide seed treatments but comparisons of seed treatments are difficult because stand responses are often erratic in the field. The objective of this study was to determine the efficacy of soybean fungicide seed treatments in naturally infested soils under controlled environments at three temperatures. Seed of three soybean cultivars were treated with six fungicide treatments or not treated and planted in two soil types collected from two fields in April, May, and June 2008 and 2009. Tests were conducted in growth chambers at 21°C (April planting), 25°C (May planting), or 28°C (June planting). Stands were determined when at least 25% of the seedlings reached the V4 growth stage. Seed treatments improved stands at all three temperatures, in both soils, and in both years. In general, the broad-spectrum fungicides trifloxystrobin + metalaxyl and mefenoxam + fludioxonil + azoxystrobin resulted in the highest stands. The selective fungicide treatments metalaxyl and pentachloronitrobenzene + carboxin were effective at all three temperatures, implying that Pythium spp. and Rhizoctonia solani, respectively, were involved in seedling disease and active over a range of temperatures. The efficacy of fungicides was not consistently associated with the cultivars used in this study.