In studies of cancer survival, Population-Based Cancer Registries (PBCRs) can provide an overview of the disease for places that have this source of information available. In Brazil, PBCR is officially available in 22 state capitals and 8 cities in the interior of the country. PBCR data from Cuiabá and Várzea Grande, state of Mato Grosso, in Midwestern Brazil, were used to estimate the survival rate of colon (C18), rectosigmoid junction (C19) and rectum (C20) cancer cases diagnosed in 2000–2009 according to the International Classification of Diseases, 10th Revision. Five-year survival rate was estimated by the unbiased and consistent net survival estimator, which is used in the country estimates of the global surveillance of cancer survival programme CONCORD Group, for all cases, and also by sex, age group, diagnosis period and place of residence. The probability of death and the number of years of life lost to illness were also estimated. The estimated standardised 5-year survival rate for colorectal cancer was 45.46% (95% CI: 43.09%–47.96%) in the cities of Cuiabá and Várzea Grande. There was no difference between the curves when the survival rate was assessed by diagnostic period (2000–2004 and 2005–2009), sex, age group or city of residence. The gross 5-year probability of death from the disease was 51.2%, accounting for 6.4% of the gross probability of death from other causes, with 2.07 being the years of life lost to illness. The results obtained for Cuiabá and Várzea Grande are compatible with survival rates estimated for Brazil in the CONCORD study, but demonstrate the need to identify reasons why we continue to have low survival rates when compared to most countries involved in the global study mentioned. The results may reflect late diagnosis, difficult access and delays in starting treatment.