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Background: Exstrophy-epispadias complex (EEC) is a complex malformation of the lower abdominal wall, bladder, and pelvic floor, which necessitates multiple successive reconstruction procedures. Surgical and infectious complications are frequent. Our aim was to evaluate kidney function in these patients. Methods: This cross-sectional study included patients with EEC, followed since birth in a pediatric urology clinic, who underwent nephrological evaluation (blood pressure (BP) measurement and blood and urine chemistries) and imaging studies (urinary tract ultrasound and DMSA kidney scan) during 2017–2020. Results: Forty-three patients (29 males), median age 9 years (interquartile range 6–19), were included. Eleven (26%) used clean intermittent catheterization (CIC) for bladder drainage. At least one sign of kidney injury was identified in 32 (74%) patients; elevated BP, decreased kidney function (estimated glomerular filtration rate (eGFR) < 90 ml/min/1.73 m2), and proteinuria/albuminuria were detected in 29%, 12%, and 36% of patients, respectively. Urinary tract dilatation (UTD) was found in 13 (37%) ultrasound examinations. Parenchymal kidney defects were suspected in 46% and 61% of ultrasound and DMSA scintigraphy, respectively. UTD was significantly associated with DMSA-proven kidney defects (p = 0.043) and with elevated BP, 39% vs. 20% in those without UTD. Decreased eGFR and elevated BP were less frequent among patients on CIC than among patients who voided spontaneously: 10% vs. 14% and 18% vs. 36%, respectively. Recurrent UTIs/bacteriuria and nephro/cystolithiasis were reported by 44% and 29% patients, respectively. Conclusion: The high rate of signs of kidney injury in pediatric patients with EEC dictates early-onset long-term kidney function monitoring by joint pediatric urological and nephrological teams. A higher resolution version of the Graphical abstract is available as Supplementary information [ABSTRACT FROM AUTHOR]