The aim of this study was to describe the incidence distribution of colorectal cancer in Fortaleza, Ceará State, and Porto Alegre, Rio Grande do Sul State, Brazil, and the time trend in the disease from 1990 to 1999. Mean annual age-adjusted incidence rates and estimated annual percent change were calculated by gender, using population-based cancer registries. EAPC showed an increase in the rates in Porto Alegre and Fortaleza for men, +4.2% (p = 0.14) and +9.3% (p < 0.001), and women, +4.6% (p = 0.11) and +5.3% (p = 0.15), respectively. The mean adjusted incidence rates were three times higher in Porto Alegre than in Fortaleza both for men (25.1 vs. 8.6/100 thousand) and women (19.9 vs. 7.1/100 thousand). This rise in incidence rates may be due to early cancer detection strategies, lifestyle changes, and alterations in the population age structure. A population profile similar to that of developed countries may explain the higher incidence rates in Porto Alegre. However, Fortaleza showed the largest increases during the period studied.