Purpose <p>Perineal morphometric alterations and functional outcomes in patients with hypospadias remain a subject of ongoing debate. This study aimed to evaluate the changes in anogenital distance (AGD)/anal position index (API) values and their intestinal functional impacts in relation to the severity of hypospadias in children.</p> Method <p>Fifty-one children who underwent hypospadias surgery (2014–2024) and 19 controls presenting for circumcision (June–September 2024) were assessed. Patients were classified as distal hypospadias (<i>n</i> = 31) or proximal hypospadias (<i>n</i> = 20). Posterior scrotal raphe–anus center (AGD), posterior scrotal raphe–coccyx distance, and API were measured. Constipation was evaluated using Rome IV criteria. Percentile values ​​were calculated.</p> Results <p>Patient ages (years): 7.42 ± 1.67/11.51 ± 2.79/8.8 ± 2.37 for control/distal/proximal hypospadias groups. Proximal hypospadias showed significantly lower AGD (33.39 ± 8.11&#xa0;mm) and API (0.35 ± 0.07) compared to distal hypospadias (54.79 ± 15.65&#xa0;mm; 0.53 ± 0.07) and controls (55.54 ± 15.57&#xa0;mm; 0.59 ± 0.08) (<i>p</i> = 0.042), (<i>p</i> &lt; 0.001). Constipation was strongly associated with proximal hypospadias (<i>p</i> &lt; 0.001). AGD distribution varied significantly across percentiles (<i>p</i> &lt; 0.001), whereas API distribution did not significantly (<i>p</i> = 0.587).</p> Conclusion <p>Changes in perineal morphometric parameters and their functional outcomes exhibit clinically meaningful distinctions in pediatric patients with proximal hypospadias. Furthermore, it is suggested that these perineal morphometric measurements should be taken into account in predicting and monitoring constipation status during postoperative follow-up in children with hypospadias.</p>