Background: A severe form of heterogeneous autoimmune illness called systemic lupus erythematosus (SLE) is characterised by the generation of autoantibodies against specific self-antigens. The aim of the present study is to evaluate LRRK2 and beclin-1 as autophagic markers in patients of SLE and their role in the pathogenesis. Methods: This case-control study was performed on 60 subjects, aged between 15-45 years old. Study participants were divided into two categories: Group I: comprised 30 patients with newly diagnosed SLE. Group II: included 30 apparently healthy age and sex matched subjects. Results: SLEDIA was positively associated with beclin1, LRRK2, ANA, Anti ds DNA. Beclin1 was positively associated with LRRK2, ANA, Anti ds DNA. LRRK2 was positively associated with ANA, Anti ds DNA. Detection of beclin1 relative gene expression with 84% positive predictive value (PPV), 90% sensitivity, 83% specificity. Detection of LRRK2 its relative gene expression with 81% negative predictive value (NPV), 76% PPV, 83% sensitivity, 73% specificity. Conclusions: These autophagic markers (LRRK2 and beclin1) correlate positively with the disease activity and severity and may have a role in disease pathogenesis and progression.