Most, but not all, studies have found that women with a high urinary 2-hydroxyestrogen (2OHE) to 16alpha-hydroxyestrone (16alphaOHE1) ratio are at reduced risk for breast cancer and have a better prognosis. The aim was to identify factors associated with the pre-operative 2OHE to 16alphaOHE1 ratio and factors that predicted the change in the ratio between the pre-operative visit and first follow-up visit three to six months post-operatively among 59 women with primary ER positive breast cancer tumors. Body measurements, questionnaires and blood samples for measurements of the 2OHE and 16alphaOHE1 plasma levels and CYP1A2 *1F genotyping were collected at both visits. Post-operatively, 15 women received tamoxifen, 30 women tamoxifen and radiotherapy concomitantly, and 14 women radiotherapy. The pre-operative ratio was not correlated with tumor characteristics, but was significantly higher in women who consumed three or more cups of coffee daily (p = 0.009). The number of CYP1A2 *1F C-alleles was correlated with a lower ratio at both visits (p = 0.13 and p = 0.02, respectively). The ratio increased between the two visits in 69.5% of the women. The factors associated with a significant increase in the ratio were concomitant tamoxifen and radiotherapy (p = 0.006), increasing alcohol consumption (p = 0.006), and a high coffee consumption (p = 0.03), but not age or CYP1A2 *1F genotype. In this pilot study, breast cancer patients who started tamoxifen during radiotherapy and who had a moderate coffee and alcohol consumption demonstrated a significant improvement in their estrogen metabolite profile between the pre- and post-operative visits.