Background Aldehyde dehydrogenase-1 (ALDH1) is involved in the regulation of cell proliferation and differentiation. Moreover, it is a marker for cancer stem cells (CSC). As CSCs were shown to be the driving force of tumor progression and metastases we suspected that the expression of ALDH1 correlated with the prognostic 5 year survival of colorectal cancer. Methods ALDH1 expression was analyzed in a highly stratified collective of 186 T3 N0 M0 G2 primary colorectal cancer specimens applying immunohistochemistry. For the analysis a scoring system for the expression of ALDH1 was developed that was aided by the pattern of the subcellular expression of beta-catenin which is a well known indicator for colorectal CSCs. Results First, ALDH1 expression could be assigned to two groups which correlated with the absence or presence of nuclear beta-catenin expression. Second, ALDH1 group 2 expression patterning correlated highly significantly with low long term survival (p = 0.010) of patients with T3 N0 M0 G2 colorectal cancer. This correlation was found univariately and when applying the multivariate Cox-model. Conclusion ALDH1 expression pattern is an independent prognostic marker for survival of T3 N0 M0 G2 colorectal cancer patients.