A principal hypothesized mechanism underlying breast carcinogenesis involves oestrogen-induced cell proliferation. In addition to its well-established role in the transcriptional regulation of genes required for adipocyte differentiation, the peroxisome proliferator-activated receptor gamma (PPARgamma) may be involved in transcriptional down-regulation of aromatase, a key enzyme in oestrogen biosynthesis. Furthermore, specific agonists for PPARgamma induce differentiation and suppress markers of malignancy in breast cancer cells in vitro. We investigated the association of the Pro12Ala PPARgamma polymorphism with breast cancer in a case-control study nested within the prospective Nurses' Health Study. Included were 725 incident cases of breast cancer diagnosed after blood collection through 1996 and 953 matched controls. In addition to breast cancer, the association of the PPARgamma Pro12Ala polymorphism with breast cancer risk factors, body mass index (BMI), weight gain since age 18 years, plasma hormones [oestrone sulphate, oestrone, oestradiol, androstenedione, testosterone, dehydroepiandrosterone (DHEA) and DHEA sulphate] and plasma lipids (total cholesterol and high density lipoprotein) was analysed. No significant association was observed between PPARgamma Pro12Ala polymorphism and either incident breast cancer (odds ratio = 1.08, 95% confidence interval = 0.85-1.38 for Ala allele carriers compared to non-carriers), plasma hormones, plasma cholesterol, BMI, weight gain since age 18 years or waist-to-hip ratio. To our knowledge, this is the first study to investigate the role of the Pro12Ala PPARgamma polymorphism in cancer. We did not find evidence to support a role for this polymorphism in breast cancer susceptibility. Furthermore, similar to others, we did not find evidence to suggest that Pro12Ala PPARgamma polymorphism is directly associated with body mass or weight gain.