The aim of the present study was the evaluation of the influence of cancer stem cells and other parameters in stage IV colorectal cancer patients. One hundred patients were retrospectively included in the study and 24 variables were examined for their relation with response to treatment and survival. A low ploidy score in the histology of colorectal cancer was associated with improvement of performance status and response to therapy. No significant correlations between the percentage of cancer stem cells from the same tissue and the remaining clinical parameters was revealed. In the multivariate analysis of all the examined parameters in Cox models, independent unfavorable prognostic factors were increased ploidy score, existence of bone metastases, use of epoetin, and existence of side-effects such as anorexia, mucositis, and weight loss. Our findings emphasize on the prognostic role of ploidy in advanced colorectal cancer, but further analysis is required to evaluate the role of cancer stem cells.