Aims The impact of MMP-1 (-519A/G, -1607 1G/2G), MMP-3 Lys45Glu (A/G), MMP-7 -181A/G, and MMP-12 -82A/G variants and plasma MMP levels on obesity and microvascular reactivity in Tunisians. Methods Our population included 202 nonobese and 168 obese subjects. Anthropometric, biochemical, and microvascular parameters were determined according to standard protocols. PCR-RFLP and ELISA were used to determine the genetic variants and levels of MMPs, respectively. Results The MMP-3 45Glu (G) allele associates with higher anthropometric values and MMP-3 levels compared to AA genotype carriers (BMI (kg/m2): 30 ± 0.51 versus 27.33 ± 0.8, P = 0.004; MMP-3 levels: 7.45 (4.77–11.91) versus 5.21 (3.60–10.21) ng/ml, P = 0.006). The MMP-12 -82G allele was also associated with higher BMI values when compared to subjects carrying the AA genotype (31.41 ± 0.85 versus 28.76 ± 0.43, P < 0.001). Individuals carrying the MMP-3 45G or MMP-12 -82G variants were also associated with a higher risk for severe forms of obesity (MMP-3: OR = 1.9, P = 0.002; MMP-12: OR = 2.63, P = 0.003). Similarly, the MMP-7 -181G allele was associated with a higher MMP-7 level and an increased risk for morbid obesity when compared to AA genotype carriers (0.32 (0.31–0.60) versus 0.18 (0.17–0.24) ng/ml, P = 0.01; OR = 1.67, P = 0.02, resp.). Conclusion MMP-3, MMP-7, and MMP-12 polymorphisms associate with obesity risk and its severity.