The effects of dietary soy protein compared to casein were examined in male and female CD1-pcy/pcy (pcy) mice with polycystic kidney disease. Animals 10 wk of age were fed purified diets containing either soy protein isolate or casein given at a level of 17.4 or 6% protein. After 13 wk on the diets, body weights and serum concentrations of albumin and protein indicated that protein nutrition was adequate on all diets. Overall, animals fed soy protein versus casein had 28% lower (P = 0.0037) relative kidney weights (g/100 g body wt), 37% lower (P = 0.0089) cyst scores (% cyst area x relative kidney weight), and 25% less (P = 0.0144) kidney water (g). Dietary protein reduction resulted in 30% lower (P = 0.0010) relative kidney weights, 25% lower (P = 0.0327) cyst scores, and 35% less (P = 0.0001) kidney water. Analysis of interactions between main effects revealed that the effects of soy protein on kidney size were significant only in females, and that effects of soy protein on cyst score were significant only in animals on the low protein diets. In addition, differences in kidney weights and cyst score due to protein reduction were significant in animals fed soy protein, but not in those fed casein as the protein source. These results show that both dietary protein source and level significantly affect polycystic kidney disease in pcy animals, with the effects of dietary soy protein being most pronounced in female animals fed the low protein diets and the effects of protein reduction being most pronounced in animals fed soy protein-based diets.