Our objective was to assess the relative contribution of genetic and environmental factors (particularly androgens) on circulating levels of lipid fractions and to determine the effect, if any, of polycystic ovary syndrome (PCOS) on lipid fractions. The study was carried out in the outpatient clinic of the Royal Hospital for Women, Paddington, Sydney, Australia. A group of 19 monozygotic (MZ) and 15 dizygotic (DZ) twin pairs was identified from the National Twin Register. Ultrasound clinical and biochemical parameters were used to define polycystic ovaries. Serum androgen and lipid fractions were also measured. Eleven pairs of twins (five MZ, six DZ) were scan discordant (i.e. one twin had polycystic ovaries and the co-twin did not). Serum levels of the lipoprotein fractions in twins with polycystic ovaries were not significantly different from the levels found for their co-twins with normal ovaries. There were no significant correlations between androgen-related hormones and any of the lipid measurements. Body mass index (BMI) was positively correlated with triglycerides and lipoprotein (a), and negatively correlated with high-density lipoprotein cholesterol (HDL-C). Sex hormone-binding globulin (SHBG) levels were negatively correlated with triglycerides and lipoprotein (a) and positively associated with HDL-C. Fasting insulin levels were significantly correlated with triglycerides and negatively with HDL-C. The MZ intraclass correlation exceeded that of the DZ twin pairs for all the lipid variables measured. The heritability estimates for lipoprotein (a), apolipoprotein B, total cholesterol and HDL-C were 0.95, 0.56, 0.48 and 0.54, respectively. However, the intraclass correlation coefficient for triglycerides was not significantly different between MZ and DZ twins, but maximum likelihood analysis indicated that at least 10% of the variance of the circulating triglyceride concentration is determined by genetic factors. We conclude that twins discordant for the PCOS do not have significantly different lipid fractions.