Background: Lupus nephritis is one of the most serious manifestations in SLE and it occurs in about 60% of patients. The objective of this study is to compare between serum cystatin C and cystatin C-based glomerular filtration rate (GFR) between SLE patients & control subjects, and between renal & non-renal SLE patients. Also to detect sensitivity & specificity of serum cystatin C as a marker of impaired GFR. Methods: This study was carried out on 60 subjects, 30 SLE patients & 30 apparently healthy controls. Disease activity was assessed by Systemic Lupus Erythematosus Disease Activity Index SLEDAI-2k. Serum creatinine & creatinine-based GFR and serum cystatin C & cystatin C- based GFR were estimated. Results: Serum cystatin C level was higher among the SLE patients than among the control group and the difference was highly significant (P = 0.000). No significant difference was found in serum cystatin C & cystatin C-based GFR among renal and non renal patients (P>0.05 ), and no significant difference was found in serum creatinine & creatinine- based GFR among renal & nonrenal patients. At a cut-off value of < 0.95mg/L, the sensitivity of serum cystatin C was 100% while specificity was only 5%. Conclusion: Although the sensitivity of cystatin C was higher than that of creatinine, it will not add any more benefit in the routine assessment of GFR in SLE patients.