Isoflavone concentration in soybean varies with genotype, soil fertility and climate. Past research indicates that temperature during seed development influences the concentration of isoflavones. The objective of our research was to characterize the effects of temperature and precipitation during plant growth on seed isoflavone concentration of a series of cultivars representing the breeding history of short-season soybean in Canada. Fourteen cultivars released from 1930 to 1992 were grown in Ottawa from 1993 to 2005 under similar agronomic and soils conditions with only the environment changing across years. Seed was harvested, cleaned and stored at -4 C until ground and the isoflavones analysed using an NIR calibrated with HPLC measured values for the aglycone concentration of daidzein, genistein and total isoflavone. There were significant differences in all isoflavone concentrations among cultivars, years and the interaction. There were no significant correlations between oil and protein content and isoflavone concentration. Plant breeding has resulted in cultivars with higher isoflavone concentration, since modern cultivars have a higher concentration of isoflavones than their historic predecessors. Broad sense heritability for total isoflavone concentration was moderate at 0.41. Bi-plot analysis revealed that cultivars responded similarly in some years and differently in others indicated that heritability could be high or low depending upon the years chosen for the determination. Direct measurement of temperature and precipitation effects on isoflavone concentration had not been done at the time the abstract was prepared.