Rationale: Interpatient variability in montelukast response may be related to variation in leukotriene pathway candidate genes. Objective: To determine associations between polymorphisms in leukotriene pathway candidate genes with outcomes in patients with asthma receiving montelukast for 6 mo who participated in a clinical trial. Methods: Polymorphisms were typed using Sequenom matrixassisted laser desorption/ionization time-of-flight (MALDI-TOF) mass array spectrometry and published methods; haplotypes were imputed using single nucleotide polymorphism-expectation maximization (SNP-EM). Analysis of variance and logistic regression models were used to test for changes in outcomes by genotype. In addition, 2 and likelihood ratio tests were used to test for differences between groups. Case-control comparisons were analyzed using the SNP-EM Omnibus likelihood ratio test. Measurements: Outcomes were asthma exacerbation rate and changes in FEV 1 compared with baseline. Results: DNA was collected from 252 participants: 69% were white, 26% were African American. Twenty-eight SNPs in the ALOX5, LTA4H, LTC4S, MRP1, and cysLT1R genes, and an ALOX5 repeat polymorphism were successfully typed. There were racial disparities in allele frequencies in 17 SNPs and in the repeat polymorphism. Association analyses were performed in 61 whites. Associations were found between genotypes of SNPs in the ALOX5 (rs2115819) and MRP1 (rs119774) genes and changes in FEV 1 (p Ͻ 0.05), and between two SNPs in LTC4S (rs730012) and in LTA4H (rs2660845) genes for exacerbation rates. Mutant ALOX5 repeat polymorphism was associated with decreased exacerbation rates. There was strong linkage disequilibrium between ALOX5 SNPs. Associations between ALOX5 haplotypes and risk of exacerbations were found. Conclusions: Genetic variation in leukotriene pathway candidate genes contributes to variability in montelukast response. Keywords: antiinflammatory; montelukast; pharmacodynamic; pharmacogeneticMontelukast is a selective cysteinyl leukotriene 1 (cysLT 1 ) receptor antagonist (1). Montelukast is recommended as an alternative to low-dose inhaled corticosteroids for patients with mild persis- tent asthma and recommended as alternative add-on (to inhaled corticosteroids) treatment in patients with moderate persistent (step 3) and severe persistent (step 4) asthma (2). Numerous clinical trials in adults and children with asthma have established the efficacy and safety of montelukast (3, 4). However, interpatient variability in response to montelukast in both children and adults with asthma is significant, with 35 to 78% of patients receiving montelukast being classified as nonresponders (5-7). The mechanisms underlying interpatient variability in response are not clear but are believed to be due, in part, to genetic variability (8-11). Indeed, several studies have reported that promoter polymorphisms in the ALOX5 (12) and the LTC 4 synthase (LTC4S) genes contribute to variability in response to LT modifiers and LT selective antagonists (13)(14)(15)(16).Cy...