Rationale: Genome-wide association studies have shown significant associations between variants near hedgehog interacting protein HHIP, FAM13A, and cholinergic nicotinic acetylcholine receptor CHRNA3/5 with increased risk of chronic obstructive pulmonary disease (COPD) in smokers; however, the disease mechanisms behind these associations are not well understood. Objectives: To identify the association between replicated loci and COPD-related phenotypes in well-characterized patient populations. Methods: The relationship between these three loci and COPDrelated phenotypes was assessed in the Evaluation of COPD Longitudinally to Identify Predictive Surrogate End-point (ECLIPSE) cohort. The results were validated in the family-based International COPD Genetics Network (ICGN). Measurements and Main Results: The CHRNA3/5 locus was significantly associated with pack-years of smoking (P 5 0.002 and 3 3 10 24 ), emphysema assessed by a radiologist using high-resolution computed tomography (P 5 2 3 10 24 and 4.8 3 10 25 ), and airflow obstruction (P 5 0.004 and 1.8 3 10 25 ) in the ECLIPSE and ICGN populations, respectively. However, variants in the IREB2 gene were only significantly associated with FEV 1 . The HHIP locus was not associated with smoking intensity but was associated with FEV 1 /FVC (P 5 1.9 3 10 24 and 0.004 in the ECLIPSE and ICGN populations). The HHIP locus was also associated with fat-free body mass (P 5 0.007) and with both retrospectively (P 5 0.015) and prospectively (P 5 0.024) collected COPD exacerbations in the ECLIPSE cohort. Single-nucleotide polymorphisms in the FAM13A locus were associated with lung function. Conclusions: The CHRNA3/5 locus was associated with increased smoking intensity and emphysema in individuals with COPD, whereas the HHIP and FAM13A loci were not associated with smoking intensity. The HHIP locus was associated with the systemic components of COPD and with the frequency of COPD exacerbations. FAM13A locus was associated with lung function.Keywords: COPD exacerbations; nicotine addiction; high-resolution CT; genetic association analysis; emphysema Chronic obstructive pulmonary disease (COPD) is a common condition that is intimately linked with cigarette smoking and is predicted to be the third leading cause of mortality and the fifth leading cause of morbidity in the world by the year 2020 (1). COPD is characterized by the presence of airflow limitation resulting from airway inflammation and remodelling or lung parenchymal destruction with emphysema. Although COPD severity is typically determined by spirometric measures (2), there is extensive heterogeneity in the amount of emphysema, degree of functional impairment, and frequency of exacerbations among patients with COPD with the same level of airflow obstruction (3). COPD can be associated with systemic manifestations, such as cachexia, which can effectively result in impaired functional capacity, worsening dyspnea, reduced health-related quality of life, and increased mortality (4).Familial aggregation studies suggest ...