In this study, we report the experience of our center with the prognosis of vesicoureteral reflux, depending on the indications for voiding cystography, during a 12-year period. Retrospective analysis included 4302 children who were analyzed according to the indication for voiding cystography: (1) a febrile urinary tract infection, (2) urinary tract malformations on ultrasonography and (3) lower urinary tract dysfunction. Vesicoureteral reflux was found in 917 patients (21.32%; 24.1% of girls and 17.9% of boys). In group (1), reflux was found in 437/1849 cases (23.63%), group (2) in 324/1388 cases (23.34%) and group (3) in 156/1065 cases (14.65%). A significantly lower prevalence of reflux and its lower degree was found in children from group (3) when compared to other groups (p < 0.01). VURs were confirmed in over 20% of children with urinary tract malformations on ultrasonography or after a febrile urinary tract infection, suggesting the need for voiding cystography in these children. Indications for this examination in children with lower urinary tract dysfunction should be limited.