Background: The autoimmune disease systemic lupus erythematosus (SLE) is considered to have polygenic, multifactorial aetiology. TREX1 mutations are under investigations for possible significant association with some SLE forms. Objective: To find out the role of TREX1 and its variants in the genetic susceptibility to SLE among Egyptian patients and to investigate its relation to the clinical manifestations, laboratory data and disease activity in SLE patients. Methods: Fifty SLE patients, and 70 age and sex matched healthy controls were included in this study. History taking, clinical examination, laboratory investigations were recorded. Systemic Lupus Erythematosus Disease Activity Index was assessed, and TREX1 gene polymorphisms were investigated. Results: Patients in this study were 46 females (92%) and 4 males (8%), their mean age was 28.76±8.83 years, and disease duration 5.49±4.43 years. A synonymous TREX1 variant c.531C>T (p.Y177Y) has been identified in 28/50 (56%) SLE cases, whereas in 23/70 (32.9%) of the control group (p= 0.01), with minor allele frequency of 0.28 in cases and 0.16 in controls. TREX1 positive patients had more oral ulcers (p= 0.004), photosensitivity (p= 0.047), seizures (p= 0.029), neuropsychiatric systemic lupus erythematosus (NPSLE) (p= 0.045, OR=7.000, 95% CI=0.791-61.975), and chilblains (p= 0.059, OR= 10.532, 95% CI= 0.550-201.679). Thrombocytopenia was significantly more found in TREX1 positive patients (p= 0.015). Conclusion: TREX1 variant (c.531C>T) was found at higher frequency in a sample of Egyptian lupus patients. TREX1 positive patients had significantly more oral ulcers. However, no homozygous or heterozygous pathogenic variants were found among studied group of Egyptian lupus patients.