Rare genetic variants in telomere-related genes have been identified in familial, idiopathic, and rheumatoid arthritis-associated pulmonary fibrosis. Short peripheral blood leukocyte (PBL) telomere length predicts poor outcomes in chronic hypersensitivity pneumonitis (CHP). Determine the prevalence and clinical relevance of rare protein-altering variants in telomere-related genes in patients with CHP. Next-generation sequences from two CHP cohorts were analyzed to identify variants in (telomerase reverse transcriptase), (telomerase RNA component), (dyskerin pseudouridine synthase 1), (regulator of telomere elongation helicase 1), (poly[A]-specific RNase), and (TERF1-interacting nuclear factor 2). To qualify, variants were required to have a minor allele frequency less than 0.005 and be predicted to be damaging to protein function. Variant status (binary variable) was used in statistical association tests, including Cox proportional hazard models for transplant-free survival. PBL telomere length was measured using quantitative PCR. Qualifying variants were identified in 16 of 144 patients (11.1%; 95% confidence interval [CI], 6.5-17.4) in the discovery cohort and 17 of 209 patients (8.1%; 95% CI, 4.8-12.7) in the replication cohort. Age- and ancestry-adjusted PBL telomere length was significantly shorter in the presence of a variant in both cohorts (discovery: -561 bp; 95% CI, -933 to -190;  = 0.003; replication: -612 bp; 95% CI, -870 to -354;  = 5.30 × 10). Variant status was significantly associated with transplant-free survival in both cohorts (discovery: age-, sex-, and ancestry-adjusted hazard ratio, 3.73; 95% CI, 1.92-7.28;  = 0.0001; replication: hazard ratio, 2.72; 95% CI, 1.26-5.88;  = 0.011). A substantial proportion of patients diagnosed with CHP have rare, protein-altering variants in telomere-related genes, which are associated with short peripheral blood telomere length and significantly reduced transplant-free survival.