In the multivariate analysis, the 1A3 of the SFTPA2 and male sex were associated with decreased risk of HP compared to avian antigen control, p < 0.05, OR = 0.1 (1A3) and OR = 0.03 (male), whereas smoking and male sex, but none of the SFTPA1 and SFTPA2 haplotypes, appeared to decrease risk of HP compared to non-exposed healthy control, p < 0.01, OR = 0.13 (smoking) and OR = 0.03 (male). Here, SFTPA1 is linked to hypersensitivity pneumonitis.