Background: To assess multicystic dysplastic kidneys (MCDK) in children, their complications and associated congenital genitourinary anomalies. Methods: Children with unilateral MCDK, evaluated between 2012 and 2020, were analyzed. In this retrospective study, data were obtained from electronic and paper health care records. Results: There were 80 children included. Follow-up time was 8.0 +/− 5.2 years (mean +/− standard deviation). None of them had hypertension. In total, 43.8% of the children had associated congenital genitourinary anomalies, most commonly cryptorchidism and vesicoureteral reflux (VUR), and 6.3% of these children had chromosomopathy. All of them had normal kidney function except one child with dysplasia of the contralateral kidney. Urinalysis was normal in 90% of children. Extrarenal malformations occurred in 22.5% of them. We observed spontaneous involution of MCDK in 38.8% of children in the observed period. Nephrectomy was performed in 12.5% of children, at an average age of 2.0 years. Conclusions: Children with a unilateral MCDK have a very good prognosis if the contralateral kidney is normal. Associated congenital genitourinary anomalies are common. Cryptorchidism was found to be the most common associated anomaly among boys, which is unique for this study. Most of these children do not suffer from hypertension, kidney dysfunction or other complications.