As part of a breast cancer case-control study of serum hormones conducted in Columbia, MO, we included several replicate quality control samples to monitor the consistency of laboratory assays. Sera were obtained from three postmenopausal women; from each woman, three samples were placed randomly in each of nine batches with the laboratory unaware of which sample corresponded to whom. Laboratory assays for estrone (E1), estradiol (E2), testosterone, androstenedione (Adione), E1SO4, dehydroepiandrosterone sulfate (DHEAS), follicle-stimulating hormone (FSH), sex hormone binding globulin (SHBG), and percentages of free and albumin-bound E2 were done at a single academic facility. ANOVA results showed that hormone values varied considerably from one batch to the next. The overall coefficients of variation (CVs) estimated for E2, percentage of unbound E2, and percentage of albumin-bound E2 were higher than 15%, but of these, only percentage of unbound E2 had both inter- and intra-assay CVs greater than 10%. Intraclass correlations (ICC) for FSH, SHBG, and DHEAS were high, suggesting that these assays are suitable for population-based studies attempting to link hormone levels to disease risk. The ICC estimated for E1SO4 was quite low due to aberrant values reported in a single batch. For the remaining hormones, the ICCs were fair (ranging from 47% for albumin-bound E2 to 67% for Adione), and studies using these assays would require a substantial increase in the sample size to detect small case-control differences.