We have shown that dietary fish oil is protective against experimentally-induced colon cancer and the protective effect is enhanced by co-administration of pectin. However, the underlying mechanism(s) have not been fully elucidated. We hypothesized that fish oil with butyrate, a pectin fermentation product, protects against colon cancer initiation by decreasing cell proliferation and increasing differentiation and apoptosis through a p27Kip1 mediated mechanism. Rats were provided diets of corn or fish oil, with/without butyrate, and terminated 12, 24 or 48 h post azoxymethane (AOM) injection. Proliferation (Ki-67), differentiation (Dolichos Biflorus Agglutinin), apoptosis (TUNEL) and p27Kip1 (cell cycle mediator) were measured in the same cell within crypts in order to examine the coordination of cell cycle as a function of diet. DNA damage (N7-methylguanine) was determined by quantitative immunohistochemical analysis. Dietary fish oil decreased DNA damage by 19% (P=0.001) and proliferation by 50% (P=0.003) and increased differentiation by 56% (P=0.039) compared to corn oil. When combined with butyrate, fish oil enhanced apoptosis 24 h post AOM injection compared to a corn oil/butyrate diet (P=0.039). There was an inverse relationship between crypt height and apoptosis in fish oil/butyrate group (r= −0.53, P=0.040). Corn oil/butyrate group showed a positive correlation between p27Kip1 expression and proliferation (r= 0.61, P=0.035). These results indicate the in vivo effect of butyrate on apoptosis and proliferation is dependent on dietary lipid source. These results demonstrate the presence of an early coordinated colonocyte response by which fish oil and butyrate protects against colon tumorigenesis.