Abdominal aortic aneurysm (AAA) involves complex dynamic remodeling processes in the aortic wall. Gelatinases (MMP2 and MMP9) and their respective tissue inhibitors (TIMP1 and TIMP2) play a crucial role during extracellular matrix (ECM) turnover in aortic tissue. In this study we characterized associations between the haplotypes of genes encoding gelatinase/inhibitor pairs and pathways involved in AAA, a total of 100 AAA patients and 192 controls were enrolled. For males, a significant decrease in the distribution of the minor G allele of the TIMP2 rs8082025 was observed in AAA patients (p = 0.01, 23.1% controls vs. 13.1% AAA). In addition, in males, the major TIMP2 GA haplotype was associated with AAA (86.9% AAA vs. 76.9% control; p = 0.009, OR = 1.997), whereas the TIMP2 GG haplotype (7.7% AAA vs. 13.9% control) was associated with protection against AAA (p = 0.046, OR = 0.518). The minor GAGC MMP9 haplotype was related to AAA for all study subjects as well as the males only subset (p = 0.011, OR = 2.202 and p = 0.025, OR = 2.156, respectively). Small differences in the distribution of gene haplotypes could be associated with different levels of gene expression and in turn influence gelatinases activity in AAA.