In order to characterize the several isoenzymes of soybeans, they were examined with respect to the effect of the polar nature of the substrate. In general, lipoxygenase-1 was most active when presented with charged substrates such as the anionic form of linoleic acid or of potassium linoleyl sulfate, whereas lipoxygenase-2 and-3 preferred nonpolar substrates such as unionized linoleic acid, methyl linoleate, linoleyl methane sulfonate, 10,13-nonadecadieneamine, or linoleyl acetate. Linoleyl sulfate, which has been advanced as an excellent readily soluble substrate for lipoxygenase, was indeed the best substrate found for lipoxygenase-1. Lipoxygenase-2 and-3 were, by contrast, totally inactive against this substrate. The favorable response of linnoleic acid to lipoxygenase-2 and-3 at pH 6.8 was ascribed to the anomalously high pK_a value of linoleic acid compared to that of short chain carboxylic acids. The pH-activity profile obtained with lipoxygenase acting on linoleyl sulfate (which was charged at all pH values examined) was shifted to lower pH values compared to the linoleic acid activity profile. The effect of changing from the charged to the uncharged substrate, when tested against lipoxygenase-1, was to increase the K_m by an order of magnitude.