The objective in this research was to evaluate the isoflavone content and the physiological quality of seed from conventional and transgenic soybean cultivars before and after 180 days of storage. Twenty one soybean cultivars: CD 202, CD 206, CD 208, CD 213RR, CD 214RR, CD 215, CD 216, CD 217, CD 218, CD 221, BRS 184, BRS 185, BRS 214, BRS 244RR, BRS 245RR, BRS 246RR, BRS 255, BRS 257, BRS 258, BRS 261 and BRS 262, grown in the 2005/2006 crop season, were assayed. The seeds were packed in Kraft paper bags and stored at room temperature under laboratory conditions. Seeds were evaluated with respect to their germination and vigor (first germination count, accelerated aging and tetrazolium test) and their total isoflavone contents and respective aglycon forms (daidzein, genistein and glycitein),glycosides (daidzine, genistine and glycitine) and malonyl conjugates. A completely randomized block design with six replications with the treatments set out within a subplot scheme (21 cultivars x 2 storage periods) was used. The F-test was used to compare means between storage periods and the Scott-Knott test to compare cultivars for each storage period, both with a 95% probability. It was concluded that isoflavone contents differ between cultivars and show a distinct behavior throughout storage.