Several studies have associated the presence of ADIPOQ gene polymorphisms with insulin resistance, adiponectin levels, and metabolic diseases such as diabetes, although with varying degrees of correlation depending on ethnicity. Here we aim to identify individual’s susceptibility to gestational diabetes mellitus (GDM) in the presence of T45G and G276T single nucleotide polymorphisms (SNPs) within the ADIPOQ gene among Filipino pregnant women. A total of 285 pregnant women (95 GDM cases and 190 controls) were included in this study. Two ADIPOQ gene polymorphisms were genotyped using TaqMan assay. Results of SNP genotyping showed no significant differences in the frequencies of TT, TG and GG genotypes of T45G SNP between the GDM and control group [p = 1.0000, 0.6179, 0.5797; OR (95%CI) = 1.030 (0.582–1.874), 1.135 (0.683–1.828), 0.833 (0.481–1.420)]. Similarly, the frequencies of GG, GT, and TT genotypes of G276T SNP were comparable in both groups [p = 0.8002, 1.0000, 0.3466; OR (95%CI) = 1.090 (0.654–1.785), 1.022 (0.616–1.665), 0.433 (0.092–1.698)]. Moreover, although adiponectin levels were significantly decreased in GDM group (p = 0.0196) and have shown substantial negative correlations with FBS, 1-hour OGTT, 2-hour OGTT, and HOMA-IR (p < 0.05), they were not significantly different according to genotypes of T45G and G276T polymorphisms both in GDM and control group. Our results suggest that neither of the two ADIPOQ gene polymorphisms influence adiponectin levels and development of GDM in a Filipino population.