Patients with severe chronic obstructive pulmonary disease (COPD) may have varying levels of disability despite similar levels of lung function. This variation may reflect different COPD subtypes, which may have different genetic predispositions. In 304 subjects from the National Emphysema Treatment Trial, we genotyped 80 markers in 22 positional and/or biologically plausible candidate genes. Regression models were used to test for association, using a test-replication approach to guard against false-positive results. For significant associations, effect estimates were recalculated using the entire cohort. Positive associations with dyspnea were confirmed in families from the Boston Early-Onset COPD Study. The test-replication approach identified four genes—microsomal epoxide hydrolase (EPHX1), latent transforming growth factor binding protein-4 (LTBP4), surfactant protein B (SFTPB), and transforming growth factor-1 (TGFB1)—that were associated with COPD-related phenotypes. In all subjects, single nucleotide polymorphisms (SNPs) in EPHX1 (p 0.03) and in LTBP4 (p 0.03) were associated with maximal output on cardiopulmonary exercise testing. Markers in LTBP4 (p 0.05) and SFTPB (p 0.005) were associated with six-minute walk test distance. SNPs in EPHX1 were associated with carbon monoxide diffusing capacity (p 0.04). Three SNPs in TGFB1 were associated with dyspnea (p 0.002), one of which replicated in the family study (p 0.02). Polymorphisms in several genes appear to be associated with COPD-related traits other than forced expiratory volume in 1 second. These associations may identify genes in pathways important for COPD pathogenesis.