Purpose: Pemetrexed has shown varied response rates in advanced breast cancer. This randomized, double-blind, phase II study was conducted to assess the efficacy and safety of two doses of pemetrexed in a homogeneous population. A secondary objective was to identify molecular biomarkers correlating with response and toxicity. Experimental Design: Patients with newly diagnosed metastatic breast cancer or locally recurrent breast cancer received 600 mg/m 2 (P600 arm) or 900 mg/m 2 (P900 arm) of pemetrexed on day 1of a 21-day cycle. All patients received folic acid and vitamin B 12 supplementation. Results: The P600 (47 patients) and P900 (45 patients) arms had response rates of 17.0% (95% confidence interval, 7.7-30.8%) and 15.6% (95% confidence interval, 6.5-29.5%) with f50% stable disease per arm, median progression-free survival of 4.2 and 4.1 months, and median times to tumor progression of 4.2 and 4.6 months, respectively. Both arms exhibited minimal toxicity (grade 3/4 neutropenia <20%, leukopenia <9%, and other toxicities <5%). Tumor samples from 49 patients were assessed for the expression levels of 12 pemetrexed-related genes. Folylpolyglutamate synthetase and thymidine phosphorylase correlated with efficacy. Best response rates and median time to tumor progression for high versus low thymidine phosphorylase expression were 27.6 % versus 6.3 % (P = 0.023) and 5.4 versus 1.9 months (P = 0.076), and for folylpolyglutamate synthetase were 37.5% versus 10.0% (P = 0.115) and 8.6 versus 3.0 months (P = 0.019), respectively. g-Glutamyl hydrolase expression correlated with grade 3/4 toxicities: 78.6% for high versus 27.3% for low g-glutamyl hydrolase (P = 0.024). Conclusion: The two pemetrexed doses yielded similar efficacy and safety profiles. Exploratory biomarker analysis identified efficacy and toxicity correlations and warrants further evaluation.Patients with advanced breast cancer who experience tumor progression after anthracycline-and taxane-based regimens were considered unlikely to benefit from other chemotherapeutics (1). However, the development of novel agents like gemcitabine (2) and capecitabine (3) has yielded palliative improvement and survival gains. Additional development of novel, safe, and effective agents is greatly needed to further improve the palliation and survival of these patients.Several phase II studies have established the single-agent activity of 600 mg/m 2 of pemetrexed, and later, 500 mg/m 2 of pemetrexed, in patients with untreated (4), minimally pretreated (one to two prior chemotherapies; refs. 5, 6), or heavily pretreated (three to five prior chemotherapies; refs. 7, 8) advanced breast cancer. Response rates ranged from 8% to 31%, with higher rates in the 600 mg/m 2 studies with untreated or minimally pretreated patients. Although both doses yielded an acceptable safety profile, toxicities in the later 600 mg/m 2 studies were significantly reduced with folic acid and vitamin B 12 supplementation before and during treatment. In view of the heterogeneous patient popul...