Objective To investigate clinical significance of urine quaporin-1 (AQP-1) and ET-1 (endothelin-1) in children with congenital hydronephrosis. Methods A total of 40 cases of children with congenital hydronephrosis and 40 healthy children were selected as observation group and control group, respectively. Patients were sub-grouped into mild, moderate and severe group based on severity of the disease. Pre-operative morning urine, intra-operative renal pelvis urine and morning urine at the 7th day after the operation were collected for the detection of ET-1, and AQP1. Results There was no significant difference in APQ-1 between mild group and control group (P?>?0.05). Obvious increase of APQ-1 was witnessed in moderate and severe group when compared with control group. In the observation group, intraoperative levels of AQP-1 was lowered while postoperative levels of AQP-1 was increased significantly compared with pre-operation (P?0.05). Urine positive rate of ET-1 in observation group were significantly higher than that in control group (P?0.05). Conclusions AQP-1 and ET-1 may be diagnostic and prognostic markers in children with hydronephrosis.