International comparisons have indicated low colorectal cancer (CRC) survival in Estonia, compared to other European countries. The objective of this paper is to analyse long-term survival as well as staging and treatment patterns of CRC in Estonia. The analysis included all incident cases of CRC diagnosed in Estonia in 1997 (n = 546), identified through the Estonian Cancer Registry and followed up for 10 years after diagnosis. Staging and treatment data were retrospectively collected from medical records. Relative survival rate (RSR) was used to estimate the outcome. The 5-year RSR was 51% for colon cancer and 38% for rectal cancer; the corresponding 10-year RSR was 50% and 39%. We observed no excess mortality for early disease. For stages II and III, the survival was markedly higher in colon cancer (5-year RSR 79% and 66%, respectively) compared to rectal cancer (66% and 30%, respectively). Around 30% of cases were diagnosed with distant disease. Among radically operated colon and rectal cancer patients, the 10-year RSR was 90% and 70%, respectively. Most patients with available pathological information had one to four lymph nodes examined. Survival has notably improved for colon cancer, but not for rectal cancer in Estonia. High proportion of cases with distant metastasis at first diagnosis along with inadequate staging and low proportion of patients treated with curatively intended surgery and appropriate chemotherapy and radiotherapy may have contributed to this outcome. Progress could be achieved by earlier diagnosis and implementing higher standards for staging and treatment. These conclusions are likely to be relevant also for other Eastern European countries.