Background: Obstructive uropathies, tubular diseases, and chronic kidney disease (CKD) are among the many renal disorders that malnutrition is frequently associated with. However, there is little information about the frequency of renal and urinary tract issues in underweight kids. Objective: The aim of the current study was to identify the anomalies of the functioning kidney and urinary tract in hospitalized children with malnutrition. Patients and methods: A cross-sectional study was conducted on 48 kids diagnosed to have malnutrition in the Pediatric Nutrition Unit at Zagazig University Hospitals, from February 2019 to May 2020. All cases underwent thorough history taking, physical examinations, and laboratory tests to detect functional abnormalities including serum NGAL, eGFR, blood urea, serum creatinine, serum electrolytes and also urine analysis. Abdominal ultrasound was done for all patients to detect any structural abnormalities. Results: Anthropometric measurement of our patients showed that there were distributions of weight, height, chest, head, and mid-arm circumferences as 6.96 (SD 2.21), 73.41 (SD 13.1), 44.9 (SD 4.67), 44.47 (SD 4.89) and 12.24 (SD 1.62), respectively. overall mean serum NGAL was 183.8 (SD 8.63) with 62.5% abnormal, while overall mean GFR was 65.89 (SD 29.8) ml/min/1.73m2 with 60.4% abnormal, 29.2% were abnormal regarding urea, 47.9% abnormal regarding creatinine, 4.2% had pus in urine analysis and overall, 62.5% had functional outcome. Seven cases with structure abnormality were found in our study, 1 case with nephrocalcinosis and 6 cases with echogenic kidney and overall, 14.6% had structural abnormalities. Conclusion: Children who were underweight frequently had functional renal problems. Functional malnutrition is linked to disorders of the kidney and urine system.