Background: Aromatase (CYP19) catalyzes the conversion of androgens into estrogens. It is in particular involved in development, reproduction and breast cancer. One of its polymorphisms, W39R localized in the N-terminal region of CYP19, significantly decreases breast cancer risk among Japanese women and was chosen for this study. In this work, we studied the structure-function relationships between W39R polymorphism and CYP19 enzyme activity. Objective: To examine the kinetic properties of the mutant W39R recombinant protein in transfected. human cells devoid of steroidogenic activity. Methods: Expression vectors for the wild-type or the mutated R39 aromatase were transiently transfected into E293 human embryonal kidney cells. The conversions of androstenedione to estrone and of testosterone and nortestosterone to 17beta-estradiol were assayed by RIA. Expression of recombinant cDNAs was analyzed by semi-quantitative RT-PCR and immunoblotting. Results: W39R recombinant protein was devoid of aromatase activity whatever the substrate used. This absence of activity was not due to the lack of expression of the recombinant enzyme since the mRNA and protein were detected. Conclusion: Our present in vitro study shows that the R39 mutant is unable to synthesize estrogens. This work provides a novel observation, being consistent with the fact that Japanese women with the variant allele (arg) have significantly lower risk of developing a breast tumor.