Background:  This study aimed to detect two genetic polymorphisms, correlate each genotype of polymorphism with biomarker serum levels, and identify which genetic variation could increase susceptibility or be associated with the severity and mortality of Covid-19 infection by examining the following genetic polymorphisms: rs1801133 MTHFR, and rs1799889 SERPINE-1 (PAI-1). Methods: In this study, a total of 102 patients with COVID-19 (mean age 52.66±18.82) and 92 apparently healthy controls (mean age 37.88±14.19) were included. The single nucleotide polymorphisms (SNPs) in MTHFR (rs1801133) and SERPIN1 (rs1799889) were analyzed using ARMS-PCR and sequencing techniques. The levels of homocysteine (Hcy) and plasminogen activator inhibitor 1 (PAI-1) proteins were quantified using an ELISA. Results: Our findings suggest that MTHFR rs1801133 CT and TT genotypes are associated with increased COVID-19 risk and mortality. CT genotype is linked to higher susceptibility (OR = 1.56, p = 0.0009), and both CT and TT genotypes are linked to more severe illness (OR = 1.66, p = 0.018 and OR = 4.10, p < 0.001, respectively). PAI-1 rs1799889 4G/5G genotype correlates with COVID-19 risk and severity (OR = 2, p = 0.03 and OR = 2.7, p =0.04, respectively). In a subgroup, CT/TT genotypes have elevated Hcy levels compared to CC genotype (p = 0.00016). Also, 4G/5G and 5G/5G genotypes have lower PAI-1 levels than 4G/4G genotype. Conclusion: A significant association was found between gene variations in MTHFR and SERPINE1 genes and COVID-19 infection susceptibility and severity.