The purpose of this study was to determine the impact of six PGHS-2 genetic variants on obesity development and microvascular dysfunction. The study included 305 Tunisian subjects (186 normal weights, 35 overweights and 84 obeses). PCR analyses were used for allelic discrimination between polymorphisms. Prostaglandin (PGE2, PGI2), leptin, and matrix metalloproteinase (MMP1, 2, 3, 9) levels were evaluated by ELISA. Fatty acid composition was performed by gas chromatography-mass spectrometry. Our results revealed that subjects carrying the PGHS-2 306CC (rs5277) and 8473CC (rs5275) genotypes present higher anthropometric values compared to wild-type genotypes (306GG, BMI (Kg/m2): 27.11 ± 0.58; WC (cm): 93.09 ± 1.58; 306CC, BMI: 33.83 ± 2.46; WC: 109.93 ± 5.41; 8473TT, BMI: 27.75 ± 0.68; WC: 93.96 ± 1.75; 8473CC, BMI: 33.72 ± 2.2; WC: 117.89 ± 2.94). A reduced microvascular reactivity and a higher PGE2 level were also found in individuals with the 306CC and 8473CC genotypes in comparison to 306GG and 8473TT carriers (306GG, Peak Ach-CVC (PU/mmHg): 0.46 ± 0.03; PGE2 (pg/ml): 7933.1 ± 702; 306CC, Peak Ach-CVC: 0.24 ± 0.01; PGE2: 13,380.3 ± 966.2; 8473TT, Peak Ach-CVC: 0.48 ± 0.05; PGE2: 7086.41 ± 700.31; 8473CC, Peak Ach-CVC: 0.23 ± 0.01; PGE2: 13,175.7 ± 1165.8). Fatty acid analysis showed a significant increase of palmitic acid (PA) (34.2 ± 2.09 vs. 16.82% ± 1.76, P < 0.001), stearic acid (SA) (25.76 ± 3.29 vs. 9.05% ± 2.53, P < 0.001), and linoleic acid (LA) (5.25 ± 1.18 vs. 0.5% ± 0.09, P < 0.001) levels in individuals carrying the PGHS-2306CC genotype when compared to GG genotype individuals. Subjects with the 8473CC genotype showed also a significant increase of PA, SA ,and LA levels when compared to TT genotype carriers (PA: 38.02 ± 1.51 vs. 12.65% ± 1.54, P < 0.001; SA: 32.96 ± 1.87 vs. 1.38% ± 0.56, P < 0.001; LA: 26.84 ± 2.09 vs. 3.7% ± 1.54, P < 0.001). Logistic regression analysis revealed that PGHS-2306CC and 8473CC variants are significantly associated with obesity status (OR 6.25, CI (1.8-21.6), P = 0.004; OR 3.01, CI (1.13-8.52), P = 0.03, respectively). Haplotypes containing the C306:T8473 (OR 2.91; P = 0.01) and G306:C8473(OR 5.25; P = 0.002) combinations were associated with an enhanced risk for obesity development in the studied population. In conclusion, our results highlight that PGHS-2306G/C and 8473T/C variants could be useful indicators of obesity development, inflammation, and microvascular dysfunction among Tunisians.