Patients with ulcerative colitis (UC) have a higher incidence of colorectal cancer. UC-associated colorectal cancer is thought to develop in patients with preexisting UC-associated dysplasia. It is crucial to diagnose UC-associated dysplasia and early stage of cancer in patients with long-standing UC for the purpose of treatment of UC-associated neoplasia. However, it is difficult to detect UC-associated dysplasia and the early stage of cancer endoscopically, and to discriminate these neoplasias from inflammatory regenerative epithelium pathologically. The aim of this study was to clarify whether observation of the surface microstructure could aid in the detection of UC-associated neopalsia, and whether analysis of genetic alterations could be used to discriminate between UC-associated neoplasia and inflammatory regenerative epithelium. Tissue samples were obtained from colectomy specimens from eight cases of UC-associated neoplasia. We examined the surface microstructure of these tissues using stereomicroscopy. We also investigated mutation of K-ras codon 12 using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and alteration of the p53 gene, using immunohistochemistry and PCR-single stranded conformation polymorphism (PCR-SSCP). The surface microstructure of UC-associated neoplasia revealed a packed distribution of oval and/or, club-shaped and/or, branch-shaped pits and a villous appearance. Nuclear accumulation of p53 protein occurred in 59.5% of UC-associated neoplasia. Mutations of the p53 exon 5-8 were detected in 95.2% of UC-associated neoplasia, and these mutations were detected in 92.9% of UC-associated neoplasia that showed negative p53 immunohistochemical staining. Mutations of the p53 exon 5-8 in regenerative epithelium occurred infrequently. The K-ras mutation rate in UC-associated neoplasia was 7.4%. In conclusion, immunohistochemistry and PCR-SSCP analysis of p53 would be useful tools for pathological discrimination between UC-associated neoplasia and inflammatory regenerative epithelium, and observation of the surface microstructure may contribute to accurate endoscopic detection of UC-associated neoplasia.