Objective Serum cystatin-C (SCysC) and microalbuminuria are well-recognized early markers of renal damage. This study aims to assess whether these early markers are elevated in children with obesity and normal serum creatinine (SCr). Methods Pediatric patients diagnosed with obesity were included (n = 105, ages 4-18 y) in this study. The patients were divided into three groups as follows: solely obese, metabolic syndrome and type 2 diabetes. Serum cystatin-C, 24-h microalbuminuria, SCr and glomerular filtration rate (GFR) were evaluated in all patients. All patients were examined with history, physical examination, laboratory analysis and ultrasonography evaluation. Results The findings showed that renal function, GFR and SCr levels were normal in all patients. There was microalbuminuria in six patients and SCysC was elevated in eight patients. There were also both elevated SCysC and microalbuminuria in eight patients. Significant elevations of both microalbuminuria and SCysC were detected in cases with type 2 diabetes (p < 0.05). Conclusions The findings suggest that SCysC may have a diagnostic value in early-renal insufficiency. Although there was not any statistically significant difference between groups in GFR, significant elevations for both microalbuminuria and SCysC in patients with type 2 diabetes were detected. This suggests that the risk factors of diabetes may have a direct relation with renal damage. Regarding renal function in type 2 diabetic and obese pediatric patients, microalbuminuria and SCysC may be screened to observe early-renal damage, even in cases with normal GFR and SCr levels.