Background Primary vesicoureteral reflux (VUR) is a common congenital anomaly of the kidney and urinary tract (CAKUT)in childhood.The present study identified the possible genetic contributions to primary VUR in children.Methods Patients with primary VUR were enrolled and analysed based on a national multi-center registration network(Chinese Children Genetic Kidney Disease Database,CCGKDD) that covered 23 different provinces/regions in China from 2014 to 2019.Genetic causes were sought using whole-exome sequencing (WES) or targeted-exome sequencing.Results A total of 379 unrelated patients (male:female 219:160) with primary VUR were recruited.Sixty-four (16.9％)children had extrarenal manifestations,and 165 (43.5％) patients showed the coexistence of other CAKUT phenotypes.Eighty-eight patient (23.2％) exhibited impaired renal function at their last visit,and 18 of them (20.5％) developed ESRD at the median age of 7.0 (IQR 0.9-11.4) years.A monogenic cause was identified in 28 patients (7.39％).These genes included PAX2 (n =4),TNXB (n =3),GATA3 (n =3),SLIT2 (n =3),ROBO2 (n =2),TBX18 (n =2),and the other 11 genes (one gene for each patient).There was a significant difference in the rate of gene mutations between patients with or without extrare-nal complications (14.1％ vs.6％,P =0.035).The frequency of genetic abnormality was not statistically significant based on the coexistence of another CAKUT (9.6％ vs.5.6％,P =0.139,Chi-square test) and the grade of reflux (9.4％ vs.6.7％,P =0.429).Kaplan-Meier survival curve showed that the presence of genetic mutations did affect renal survival (Log-rank test,P=0.01).PAX2 mutation carriers (HR 5.1,95％ CI 1.3-20.0;P=0.02) and TNXB mutation carriers (HR 20.3,95％CI 2.4-168.7;P =0.01) were associated with increased risk of progression to ESRD.Conclusions PAX2,TNXB,GATA3 and SLIT2 were the main underlying monogenic causes and accounted for up to 46.4％of monogenic VUR.Extrarenal complications and renal function were significantly related to the findings of genetic factors in children with primary VUR.Like other types of CAKUT,several genes may be responsible for isolated VUR.