Abstract Context The ontogeny of hypospadias and its implications remain incompletely understood. Objective To examine whether fetal outcomes and reproductive hormone concentrations in boys with hypospadias differ from reference standards during minipuberty. Design Prospective cohort study (May 2021-January 2023). Setting Tertiary hypospadias center. Patients Infants presenting with hypospadias (n = 139), of whom 113 were enrolled following parental consent (median postnatal age: 0.28 years). Interventions Examination of hypospadias grade, external masculinization score (EMS), placental and birth weight, and blood sampling (reproductive hormones). Main Outcome Measures Fisher's exact test assessed gestational age (GA)-specific birth weight and placental centiles by hypospadias severity. GA-specific reproductive hormone concentrations were converted to SD scores (SDSs) according to an established reference standard for healthy Danish boys. The 1-sample Wilcoxon signed-rank test compared concentrations to 0 SDS. Results Eighty-nine boys (79%) had distal hypospadias with a median EMS of 11 while median EMS was 9 in boys with proximal hypospadias. Birth weight and placental centiles were lower in boys with proximal hypospadias (P = .014 and P = .038). The median concentrations of FHS (0.83 SDS), testosterone (0.71 SDS), and free testosterone (0.83 SDS) were higher in boys with hypospadias compared to 0 SDS (P < .001). The median concentrations of inhibin B (−0.38 SDS), anti-Müllerian hormone (AMH) (−0.23 SDS), insulin-like factor 3 (INSL3) (−0.31 SDS), androstenedione (−0.52 SDS), and dehydroepiandrosterone sulfate (−0.50 SDS) were significantly lower. LH, SHBG, 17-hydroxyprogesterone, and dihydrotestosterone were not statistically different. Hormone SDS did not differ significantly by hypospadias severity. Conclusion Hypospadias severity was significantly associated with birth and placental weight centiles. Testicular Sertoli cell markers (AMH and inhibin B) and the Leydig cell-derived INSL3 were reduced, suggesting subtle testicular dysfunction in boys with hypospadias during minipuberty. Further research to identify implications for future reproductive health is warranted.