Background The occurrence of distant metastases in colorectal cancer (CRC) is the most important parameter in assessment of the prognosis of patients with CRC. Epithelial–mesenchymal transition (EMT) is the process that is incriminated in the occurrence of metastatic spread in CRC. Snail-1 is a zinc-finger transcription factor that is responsible for the induction of the EMT. Cancer stem cell hypothesis pointed to the presence of certain cells that are responsible for metastasis and recurrence of cancer. Aldehyde dehydrogenase 1 (ALDH1) is a previously discovered cancer stem cell biomarker that is involved in cellular proliferation and drug resistance. Tight junction proteins play many roles in proliferation and neoplastic transformation of cells. Claudin-1 is a universal marker of tight junctions and is associated with progression of various cancers. In this study, we aimed to determine whether EMT markers, the expression of stem cell markers, and levels of the tight junction proteins are associated with the clinical and pathological features and clinical prognosis of patients with CRC by evaluating tissue protein expression of Snail-1, ALDH1, and claudin-1. Patients and methods Expressions of Snail-1, ALDH1, and claudin-1 were evaluated in sections from 50 paraffin blocks that were retrieved from 50 patients having CRC. We have followed up the patients for 3 years. We correlated expression of markers with clinical, pathological, and follow-up parameters. Results Both Snail-1 and ALDH1 are overexpressed in CRC cells mainly in tumors located in the ascending colon (P = 0.012 and 0.003, respectively), and their expression was directly correlated with high grade (P = 0.002 and 0.005, respectively), larger tumor size (P = 0.031 and 0.007, respectively), presence of lymph node metastasi