Purpose CT has been found superior to chest x-ray to detect lung malignances. However, indeterminate lung lesions (ILL) are found in 4-42% by using CT in staging colorectal cancer (CRC) patients. Our aim was to examine the frequency of ILL on staging CT and the rate of the ILL being malignant, and to investigate if PET/CT was useful in pointing out the malignant cases. Methods A prospective analysis of 238 consecutive patients operated for CRC followed median 24 months. All the patients had a preoperative staging CT. Patients with ILL had a PET/CT scan performed 3 months postoperatively and low dose chest CT performed 6, 12, 18 and 24 months postoperatively. Results Twenty percent of the patients had ILL. Four of these patients (8.5%) had lung metastases detected median 9 months postoperatively, while 2 (4.3%) had other lung malignancies. One patient had TB. In patients with normal staging chest CT 10 of the 185 patients (5.4%) developed lung metastases detected median 16 months postoperatively. This was significantly later than in patients with ILL (p < 0.001), but with regard to the number of patients developing lung metastases no significant difference was found between the groups (p = 0.12). Conclusions Even though a relative low number of ILL turn out to be malignant it seems advisable to use PET/CT scan in the follow-up to detect lung metastases as early as possible to better the prognosis. For the same reason all CRC patients should have chest CT included in their follow-up 6-12 months postoperatively.