In the single SNP model, we observed that rs1136451 of the SFTPA1 was associated with increased HP risk, p = 0.02, OR = 11.4 (2.3–57.9), whereas rs1136450 of SFTPA1 and rs1130866 of SFTPB were associated with lower risk of HP, p = 0.02, OR = 0.2 (0.0–0.6) compared to non-exposed controls. Here, SFTPB is linked to hypersensitivity pneumonitis.