Background <p>Circulating tumor cells (CTCs) has been proven to be related to the prognosis of cancer. Nevertheless, there are very few studies on the prognostic significance of CTCs in colorectal cancer (CRC). In this study, we investigated the impact and clinical significance of the number of circulating tumor cells (CTCs) and the expression of glioma-associated oncogene 1 (Gli1) on the prognosis of colorectal cancer (CRC).</p> Methods <p>This study encompassed a total of 310 colorectal cancer patients who had not received radiotherapy or chemotherapy. Simultaneously, the circulating tumor cells of these 310 patients were isolated and enumerated. The expression of Gli1 in circulating tumor cells (CTCs) was determined by in situ hybridization with RNA (RNA-ISH) method. The results were analyzed in combination with the clinical and pathological parameters of the patients as well as their treatment outcomes. Survival analysis was also conducted to determine its prognostic significance.</p> Results <p>Gli1 expression was found in 23.15% patients at baseline. Patients with Gli1 expression had significantly poorer treatment response and metastasis. Besides, Gli1 on CTCs was an independent prognostic indicator for poorer progression-free survival and overall survival.</p> Conclusions <p>The study demonstrated that Gli1 expression and CTC count are promising prognostic indicators in patients with CRC. Further studies are needed to clarify the value of integrating the indicator with current clinical strategies in improving the survival of CRC patients.</p>