We studied reproductive outcomes in a cohort of 7,450 pregnancies identified through three Kaiser-Permanente facilities in the San Francisco Bay Area, in relation to exposure to the pesticide malathion, applied aerially to control an infestation by the Mediterranean fruit fly. We included in the cohort all women over age 17 who were registered at these facilities and who were confirmed as pregnant during the spraying period. Residence histories throughout the pregnancy were obtained by mailed questionnaire or telephone interview from 933 women with adverse outcomes and a sample of 1,000 women with normal outcomes, and were converted to geographical coordinates. We linked the coordinates for malathion spraying corridors with the residence coordinates to create individual exposure indices for each week of pregnancy. The statistical analysis compared each of the adverse pregnancy outcome groups against an appropriate control group using logistic regression or survival time regression approaches. After adjustment for various confounders, no important association was found between malathion exposure and spontaneous abortion, intrauterine growth retardation, stillbirth, or most categories of congenital anomalies. Gastrointestinal anomalies were related to second trimester exposure (odds ratio = 2.6), based on 13 cases and not specific to any particular International Classification of Diseases code.