The goal of this study was to determine the prevalence of the testicular, epididymal, and vasal anomalies (TEVA) in cryptorchid and communicating hydrocele pediatric patients. Six hundred and ninety-one prepubertal boys underwent inguinal exploration for 741 undescended (UDT) or hydrocele testes. Two hundred and fifty-five TEVA were detected in 154 UDT boys, compared to 32 defects in 24 hydrocele patients (p < 0.001). The TEVA were more frequent in bilateral UDT (p = 0.009). Multiple defects were observed more frequently in the intra-abdominal testicles (p = 0.028). A correlation was found between the testicular atrophy index (TAI) and the incidence and number of TEVA in the UDT boys (p < 0.001). The smaller the testis (higher TAI), the more the defects that appeared in it and the higher the frequency of their appearance. Another correlation was established between testis position and the incidence and number of TEVA (p < 0.001). The higher the testis position, the more the defects that appeared in it and the higher the frequency of their appearance. A correlation was established between the position and the volume of the affected testis (p < 0.001). The higher the gonad position, the more severe the atrophy observed in it. The TEVA were more frequent in the UDT boys than in the hydrocele patients. We revealed that the risk of abnormal fusion between the testis, epididymis, and vas deferens is connected with the testis position (intra-abdominal testes) and bilateral non-descent.