Our recent study has demonstrated that brain (fetal)-type glycogen phosphorylase (BGP) positive foci (BGP foci) have a vital role in the de novo colorectal carcinogenesis. This paper reviewed the investigation on the genetic alternations in the BGP foci and the clarification of the mechanisms of de novo colorectal carcinogenesis. De novo colorectal carcinomas with invasion into submucosa or superficial muscularis propria were selected from resected specimens. Investigations of the p53, K-ras and APC mutations were performed in the BGP foci, BGP negative colorectal mucosa and de novo colorectal carcinoma. No K-ras mutation was observed in all of the cases. Mutations of p53 and APC were 14 (50.0%) and 9 (32.1%) in de novo colorectal carcinomas, and 11 (39.3%) and 1 (3.6%) in BGP foci, respectively. Both p53 and APC mutations were detected in 8 and 1, p53 mutation alone in 6 and 10, APC mutation alone in 1 and 0 out of 28 de novo colorectal carcinomas and BGP foci, respectively. Our sequential studies propose that the two major pathways, i.e., the p53-APC pathway and the p53 alone pathway in the de novo colorectal carcinogenesis.