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Despite advances in therapy, outcomes for children with pulmonary hypertension remain poor. We sought to assess the validity of a pediatric-specific functional classification system for pulmonary hypertension (PH) in a heterogeneous population of children with PH diagnosed by echocardiogram or cardiac catheterization. A single-center, retrospective study of 65 infants and children with PH was performed. Pediatric Functional Class (FC) at diagnosis, at last visit, and change in FC over time were evaluated for their association with mortality and PH-associated morbidity in univariate, time-to-event, and multivariate regression analyses. Median age at PH diagnosis was 5.3 months (0 days-12.7 years). Twenty-five children (38 %) had idiopathic PH or PH secondary to congenital heart disease, one (2 %) had left heart disease, and 39 (60 %) had PH secondary to respiratory disease. Mortality was 25 % (16/63), primarily in the first year of follow-up. FC at diagnosis was not significantly associated with survival (p = 0.22), but higher FC (more impaired) at last visit (p < 0.001) and change in FC over time (HR 2.3, 95 % confidence interval 1.3-4, p = 0.0003) were associated with mortality. Higher FC at last visit was associated with greater days of hospitalization in the intensive care unit per year (p = 0.006) and history of cardiac arrest (p = 0.012) and syncope (p = 0.02). Although pediatric FC at diagnosis was not predictive of mortality, response to therapy (as assessed by change in FC over time and FC at last visit) was associated with morbidity and mortality in this heterogeneous cohort. Multicenter prospective studies are necessary to further validate these findings.