This population-based case-control study assessed the effect of current cigarette smoking on the risk of functional ovarian cyst development. Cases were all 15-39 year-old enrollees of Group Health Cooperative of Puget Sound (GHC) who had either an inpatient primary diagnosis of functional ovarian cyst in 1988 or 1989 (n = 61) or an outpatient primary diagnosis of functional ovarian cyst at five GHC primary care clinics (n = 37). Controls were randomly selected enrollees matched to cases on age, primary care clinic, and enrollment date (n = 239). A total of 36.7% of cases and 20.5% of controls were determined by medical record review to be current smokers. Compared with women who were not current smokers, the relative risk of a diagnosed functional ovarian cyst among smokers was 2.0 (95% confidence interval 1.1-3.5). This finding, in an area of little previous research, provides a promising lead in the investigation of the etiology of functional ovarian cysts and the effects of smoking on ovarian function in general.