RUNX3 is a tumour suppressor gene that plays an important role in the development of various cancers. The present study aimed to compare RUNX3 mRNA expression levels and DNA copy numbers in the non-neoplastic rectal mucosa between ulcerative colitis (UC) patients with and without UC-associated colorectal cancer (UC-Ca). We further aimed to build a predictive model of the development of UC-Ca based on the RUNX3 DNA copy number. RUNX3 mRNA expression levels were quantified by RT-PCR. The hypermethylation and DNA copy number of RUNX3 were also determined. Thirty-five UC patients were examined, 17 of whom had UC-Ca (UC-Ca group) and 18 who did not (UC-NonCa group). The UC-Ca group had significantly lower mRUNX3 expression levels and smaller DNA copy numbers than the UC-NonCa group (p=0.04, p=0.0016, respectively). RUNX3 expression levels correlated with DNA copy numbers. Classification of the UC-Ca and UC-NonCa group based on DNA copy number gave an accuracy of 82.9%. RUNX3 expression levels in the non-neoplastic rectal mucosa was significantly decreased in the UC-Ca group and it is suggested that this was attributable to the decrease in RUNX3 DNA copy number. The present predictive model may be useful in the selection of high risk UC-Ca patients and to improve the efficacy of surveillance colonoscopy. The present study suggests that RUNX3 might play an important role in the development of UC-Ca.