Early diagnosis for colorectal cancer (CRC) by monitoring of gastrointestinal epithelial cells is a possible direct approach. Although human faeces form a heterogeneous mixture of gastrointestinal mucosal epithelial cells and other materials, we have developed a method to purify total RNA from human stool samples. The gene for faecal cytokeratin 19 (CK19) was highly expressed in stools from patients with metastatic CRC, but not from patients with non-metastatic CRC or from normal individuals. Thus, purified faecal RNA can be used for the detection of differentially expressed genes. This technique may help identifying meaningful faecal RNA markers for the non-invasive screening of patients with CRC.