The main aim of our study was to determine if the ACE2 rs2106809 and AGT rs699 polymorphisms increase the risk and severity of Covid-19 infection in Iraqi patients. This case-control study included 102 patients (mean age 52.66±18.82 years) and 92 healthy (mean age 37.88±14.19 years). The patients were grouped based on severity: hospitalized (n = 57) and non-hospitalized (n = 45). Demographic and comorbidity data was also collected. Genotype distribution of two selected SNPs ACE2 gene rs2106809 and AGT rs699 polymorphisms was performed by allele-specific PCR (AS-PCR) and sanger sequencing. The ACE2 rs2106809 C allele was associated to an increased risk of Covid-19 infection and the severity in males but not in the females (C vs. T OR = 3.04 p=0.01 and C vs. T OR = 4.9, p = 0.03, respectively). While AGT rs699 TC genotype was associated with 2.96 folds higher risk of Covid-19 infection (TC vs.TT, CC OR =2.96, 95%CI = 1.12–6.44; p = 0.02).  The AGT rs699 was not associated with the severity of infection. Among outpatients, benign conditions were associated with a lower risk, however older age males and comorbidities increased the risk. We concluded that the genetic variant of rs2106809 ACE2 in males was significant with a risk of infection and severe clinical course because it could be located on the X-chromosome, and at the same time AGT rs699 polymorphism had an impact on the increased risk of Covid-19 but had no relation with the severity of Covid-19.