The role of urinary toxins in interstitial cystitis (IC) has been suggested. This report describes the partial purification of a substance from human urine that inhibited in vitro colony formation by mouse fibroblasts. Urine samples from 15 women with IC and 17 healthy women serving as volunteers were fractioned by ultrafiltration and chromatography methods and tested by the inhibition of Swiss 3T3 fibroblast colony formation. The fibroblasts were cultured at low density with varying concentrations of whole or fractioned urine. Colonies were counted at 10 days. Colony formation was reduced by incubation with whole urine, ultrafiltrate, and nonadsorbed C18 fractions. Inhibition of colony formation by urine from healthy volunteers or women with IC was not significantly different. In vitro colony formation by Swiss 3T3 cells was inhibited by a component of human urine. The toxicity of urine from IC patients was not different from that of urine from healthy controls.