<i>Background:</i> The tumour-associated trypsin inhibitor TATI is expressed together with trypsin in many cancer forms, and an elevated serum level associates with poor prognosis. TATI can reduce tissue destruction by inhibiting trypsin and other proteinases, and in some cancer forms, its high tissue expression is associated with favourable prognosis. We analyzed the prognostic values of TATI, trypsinogen-1 and trypsinogen-2 immunoexpression from tissue array blocks constructed from surgical specimens of 592 colorectal cancer patients. <i>Results:</i> TATI positivity correlated negatively with differentiation (p < 0.001) and positively with the histological type of adenocarcinoma (p < 0.001). Trypsinogen-1 and trypsinogen-2 positivity correlated with Dukes’ stage (p = 0.045, p = 0.050); the percentage of trypsinogen-1- and trypsinogen-2-positive tumours was lower in metastasized (Dukes’ stage C–D) than in local (Dukes’ stage A–B) disease. In addition, trypsinogen-2 correlated inversely with differentiation (p = 0.012). In univariate analysis, the expression of TATI associated with more favourable cancer-specific survival (p = 0.010). In multivariate analysis, low TATI (p = 0.044), age (p < 0.001), Dukes’ stage (p < 0.001), tumour differentiation (p = 0.020) and location in the rectum (p = 0.006) were independent prognostic factors for adverse outcome. Furthermore, TATI expression was an independent prognostic factor in a subgroup of trypsinogen-1- (p = 0.007) and trypsinogen-2-positive (p = 0.006) tumours. <i>Conclusion:</i> TATI tissue expression is an independent prognostic marker in colorectal cancer.