Trypsin inhibitors (TI), tannins, and lectins appear to have a role in preventing chronic diseases in humans. The genetic variability of these traits in common bean needs to be ascertained in order to increase levels through breeding. The variability of TI, tannin, and lectins was determined in five bean cultivars grown at five locations in Mexico. TI and tannins contents in colored beans that belong to the Jalisco race were higher (11.1-11.9 trypsin units inhibited (TUI)/mg and 29.0-38.1 mg catechin equivalent (CE)/g, respectively) than cultivars of the Durango race (7.9-8.3 TUI/mg and 16.8-19.9 CE/mg, respectively). Bayo Victoria, a Durango race cultivar, had three times more lectins than levels reported for soybean. Cultivar influenced TI and tannins contents (p < 0.001), whereas site affected lectins (p < 0.001). An increase in levels of TI and tannins could be enhanced through breeding.