BACKGROUND: This study describes geographical differences in cancer incidence in Costa Rica, and investigates if some of these differences may be related to pesticides. METHODS: Data were combined from the cancer registry (1981-1993), the 1984 population census, the 1984 agricultural census, and a national pesticide data set. The 81 counties of Costa Rica were the units for the ecological analyses. Adjacent counties were grouped into 14 regions (3 urban and 11 rural) with relatively similar socioeconomic characteristics. County indices for population density and agricultural variables were constructed and categorized. Differences across regions and categories were assessed by comparing observed numbers of incident cases to expected values derived from national rates. Within the tertile of most rural counties, rate ratios between categories of high and low pesticide use were calculated. RESULTS: In urban regions, excesses were observed for lung, colorectal, breast, uterus, ovary, prostate, testis, kidney, and bladder cancers; and in rural regions for gastric, cervical, penile, and skin cancers. Skin cancers (lip, melanoma, non-melanocytic skin and penile cancer) occurred in excess in coffee growing areas with extensive use of paraquat and lead arsenate. In the most rural subset, heavy pesticide use was associated with an increase of cancer incidence overall and at a considerable number of specific sites, including lung cancer (relative risk [RR] 2.0 for men and 2.6 for women) and all female hormone-related cancers (RR between 1.3 and 1.8). CONCLUSIONS: Regions and populations at high risk for specific cancers were identified. Several hypotheses for associations between pesticides and cancer emerged. The findings call for studies at the individual level.