The fatty acid content of soybean seeds has not been considered when evaluating the quality of seeds in research work carried out so far. The objective was to determine the effects of absence of lipoxygenases and low linolenic acid content on seed quality after delayed harvest. Four different bulks were constructed: (a) seeds with lipoxygenase and normal linolenic acid content; (b) seeds with lipoxygenase and low linolenic acid content; (c) seeds without lipoxygenase and normal linolenic acid content and (d) seeds without lipoxygenase and low linolenic acid content. F5 seeds were harvested at the R8 stage and 10, 20 and 30 days after R8 stage. Seed physiological quality was evaluated by the standard germination test, accelerated aging test and emergence speed index. Seeds with low linolenic acid content presented higher seed quality as measured by the accelerated aging test. Seeds with lipoxygenase showed higher vigor as compared to those lacking these isozymes as determined by the emergence speed index.