Hydrochlorothiazide (HCTZ) is among the most commonly prescribed antihypertensives, yet <50% of HCTZ treated patients achieve blood pressure (BP) control. Herein, we integrated metabolomic and genomic profiles of HCTZ treated patients to identify novel genetic markers associated with HCTZ BP response. The primary analysis included 228 white hypertensives treated with HCTZ from the Pharmacogenomic Evaluation of Antihypertensive Response study. Genome-wide analysis was conducted using Illumina Omni 1M-Quad Chip, and untargeted metabolomics was performed on baseline fasting plasma samples using a gas chromatography-time-of-flight mass spectrometry platform. We found thirteen metabolites significantly associated with HCTZ systolic BP (SBP) and diastolic BP (DBP) responses (FDR<0.05). Additionally, integrating genomics and metabolomics data revealed three polymorphisms (rs2727563 PRKAG2, rs12604940 DCC, and rs13262930 EPHX2) along with arachidonic acid, converging in the netrin signaling pathway (p=1×10−5), as potential markers significantly influencing HCTZ BP response. We successfully replicated the three genetic signals in 212 white hypertensives treated with HCTZ, and created a response score by summing their BP lowering alleles. We found patients carrying one response allele had a significantly lowest response than carriers of six alleles (ΔSBP/ΔDBP: −1.5/1.2 vs −16.3/−10.4 mmHg, respectively, SBP-score p=1×10−8 and DBP-score p=3×10−9). This score explained 11.3% and 11.9% of the variability in HCTZ SBP and DBP responses, respectively, and was further validated in another independent study of 196 whites treated with HCTZ (DBP-score p=0.03, SBP-score p=0.07). This study suggests that PRKAG2, DCC and EPHX2 might be important determinants of HCTZ BP response.