Homografts have long been used for right ventricular outflow tract (RVOT) reconstruction. Tissue banks struggle to meet the clinical demand of tissue, with insufficient donor availability and strict recommendations on tissue quality with high proportions of discards. This study analyzes the long-term outcome of patients receiving a homograft with small fenestrations of the cusps or other structural changes, to evaluate if minor impairment of the homograft affects the durability. Homograft characteristics and patient outcome were described. Follow-up was maximum 24 years. Structural changes of the homografts were analyzed in relation to patient outcome, using univariable and multivariable Cox proportional hazard regression. Between 1995 and 2018, 468 patients received 535 homografts in the RVOT in Lund. Median recipient age was 13 years. There were 137 (26.9%) reinterventions. Freedom from reintervention was 75.8% (95% CI 71.3–79.7%) at 10 years and 57.4% (95% CI 50.0–64.0%) at 20 years. Small fenestrations of the cusps, fibrosis of the cusps and minor atheromatosis of the vessel did not show any statistically significant impact on long-term outcome, hazard ratio = 0.46 (95% CI 0.11–1.87, p = 0.276) and hazard ratio = 0.80 (95% CI 0.25–2.56, p = 0.704). Minor structural changes of the homografts seem to be acceptable without affecting the long-term durability.