Background: Tamoxifen is a prodrug. Its principal active metabolite endoxifen is a product of cytochrome P450 2D6 (CYP2D6) metabolism. The CYP2D6 gene is highly polymorphic with a number of relatively common reduced function alleles. The aim of this study was to determine whether plasma endoxifen levels were reflected by CYP2D6 genotype or adverse effects in individuals taking tamoxifen. Methods: Plasma endoxifen was measured by High Performance Liquid Chromatography / Mass Spectroscopy in 90 breast cancer patients taking 20mg tamoxifen per day. Ten CYP2D6 single nucleotide polymorphisms were assessed to designate four putative CYP2D6 functional categories: ultra-rapid (UM), extensive (EM), intermediate (IM) and poor (PM) metabolizers. CYP2D6 inhibitor use and adverse effects were documented. The study was part of an ongoing Australian trial of tamoxifen dose escalation. Results: There was marked variation in plasma endoxifen levels across the cohort (mean 27.6 nM, SD 14.3). Endoxifen levels were significantly associated with metabolizer categories (p<0.001, r= -0.44), but were not distinctive between categories. For example, in the EM category (n=46) endoxifen levels ranged from 3.8-72.2 nM (mean 32.6 nM) with levels in the lowest quartile (3.8-19.7 nM) substantially overlapping the PM category (n=11); 6.1-24.7 nM. Consistent with an impact of non-CYP2D6 genotype related factors on endoxifen levels, endoxifen was significantly lower in 18 patients taking CYP2D6 inhibitor medications (p=0.005). There was no association between endoxifen levels and vasomotor symptoms or other adverse effects of tamoxifen. Conclusions: Endoxifen levels were highly variable in patients taking standard dose tamoxifen, and not predicted by CYP2D6 genotype or adverse effects. Therapeutic monitoring of endoxifen levels may be a useful approach to assess tamoxifen activity.