A suite of microclimate variables affected germination of five Great Plains native plants seeded on an extensive green roof. Germination was significantly (~' = 0.05) greater in a greenhouse control versus the green roof for shortbeak sedge and prairie spiderwort (Carex brevior (35% versus 23% Tradescantia occidentalis 19% versus 0%). No significant germination difference between the greenhouse and green roof existed for two, warm-season species, Liatris squarrosa and Eragrostis spectabilis. Significant differences in microclimatic conditions between green roof plot locations suggest a heterogeneous environment can decrease seed germination. This impact was attributed to differences in the receipt of solar radiant energy, surface temperature, and vapor pressure deficit. Light reflection and thermal emission from the adjacent buildings supplied additional energy in some locations (depending on time of year or time of day) that varied greatly over only a few meters. Designers must carefully analyze microclimate impacts and consider those implications for plant selection and seeding. Establishment of some native seeds in high temperature zones may take more irrigation or benefit from mulching than those in moderate temperature zones. Increased seeding rates and targeted seeding dates may also be useful strategies. Future green roof research should examine germination across steep microclimate gradients, seed a wider suite of native plants to broaden plant biodiversity, and follow seedling development and mortality.