Background: Recently it has been identified a subgroup of patients with hypersensitivity pneumonitis (HP) that develop autoantibodies with/out clinical manifestations of autoimmune disease. Genetic factors involved in this process, and the effect of these autoantibodies on clinical course are largely unknown. Matrix metalloproteinase (MMP) have an important role in the architecture and pulmonary remodeling, they have been little studied in the different HP phenotypes. Aim: To identify MMP1, MMP2, MMP9, MMP12 gene polymorphisms associated with susceptibility to HP with (HPAb+) and without autoantibodies (HP). Methods: 34 HPAb+ and 104 HP patients were included. Autoimmune laboratory profile included ANA, RF, anti-SSA/Ro, anti-SSB/La, anti-Scl70 and anti-CCP. In addition, a group of 184 healthy subjects (HC). 12 SNP were genotyped in 4 genes: MMP1, MMP2, MMP9, MMP12 using allelic discrimination by qPCR. Results: Using the dominant model of genetic association, comparisons between the three groups were performed. For rs7125062 in MMP1 (CC versus CT+TT), an association was found when comparing groups of patients with healthy subjects: HPAb+ vs. HC (p=8.6E-09, OR=10.62, CI95%=4.34-25.96); HP vs. HC (p<0.001, OR=7.85, CI95%=4.54-13.57). rs11646643 in MMP2, shows a difference in the HPAb+ group by the dominant genetic model GG vs. GA+AA, (p=1.4E-03, OR=8.11, CI95%=1.83-35.84). In the linear regression analysis, rs11646643 (GA+AA) was associated to a difference in basal/12months FVC (p=0.013, b=0.228, ci95%=1.97-16.72). Conclusions: There are SNPs associated to risk increased of developing HP, and with the evolution towards to phenotype autoantibodies-positive.