Pulmonary vascular remodeling process was analyzed using morphometry in lung biopsy specimens taken from 26 children, aged 6 to 160 months, who had congenital heart disease and significant pulmonary arterial hypertension. Reparative surgery was performed in 22 patients and palliative surgery was performed in four patients. One patient expired postoperatively and four others after hospital discharge. Vascular remodeling examination revealed a characteristic pathological picture: pronounced medial thickening with increased collagen content (fibrosis), without significant arterial intimal proliferation. At a mean follow-up of 44 months, 72% of the survivors were asymptomatic with no medication. Diagnosed by echocardiogram, 22% of these patients were shown to have pulmonary arterial hypertension. The characteristic pathological features described above occurred in 38% of the patients who either expired or had pulmonary hypertension postoperatively. These findings were an aid to identifying a high risk group in which the outcome does not meet expectations for the classical grade I and II changes. We concluded that the presence of isolated medial thickening does not ensure either survival or a normal postoperative pulmonary arterial pressure at late follow-up and that the collagen content can be a better reference for good outcome. Early intracardiac repair is recommended before the development of significant medial fibrosis.