Introduction Recent studies have identified both the prognostic and predictive utility of determining the number of circulating tumour cells (CTC) in patients with solid cancers. Material and methods In the present pilot study we evaluated the ability of two different methods to isolate CTC in combination with two strategies to enumerate CTC from patients with stages II and III surgically treated colorectal cancer (CRC). First, we used two systems for tumour cell enrichment (differential centrifugation and immunomagnetic beads), combined with two methods to enumerate CTC (real-time PCR and flow cytometry), to determine the most efficient combination. These experiments were performed in a model system using serial dilutions of HT29 tumour cell lines with lymphocytes. Then, CTC analysis using the technical approach selected before was performed in 109 blood samples from 16 stage II and III CRC patients during chemotherapy treatment and follow-up. Results Immunomagnetic beads followed by flow cytometry was the most efficient combination (ED=60.53; p=0.5). Two cases out of 16 patients analysed had clinical tumour relapse. In both, we detected a significant increase of CTC five and six months, respectively, before the relapse was clinically evidenced. An increase of CTC was also observed in another case without clinical evidence of relapse. The remaining cases (13) had very few or no detectable CTC and no clinical evidence of relapse (p=0.029). Conclusions Changes in CTC numbers during follow-up might predict tumour relapse. Further evaluation of CTC prognostic and predictive value in patients with early CRC is warranted.