BACKGROUND: Although pulmonary arterial hypertension (PAH) is widely accepted as deadly, if not a rare disease, its prognostic impact beyond reports from specialist centres is unknown. METHODS: Using the unique Scottish Morbidity Record Scheme and linked survival data, we tracked the survival of all Scottish adults aged < or =65 years admitted for the first time during the period of 1986 to 2001 with a probable diagnosis of Idiopathic PAH and a PAH related to connective tissue disorders (Connective PAH) and congenital abnormalities (Congenital PAH) - the three most common forms of PAH. RESULTS: Overall, 374 Scottish men and women were discharged from the hospital with incident PAH during the period 1986 to 2001. On an unadjusted basis, Congenital PAH (40-45%) was associated with the lowest case fatality at 5 years in both men and women. In both sexes, Idiopathic PAH and Connective PAH were associated with high initial one-year case fatality (20-30%) with a steady accumulation of fatal events in the four years thereafter (60-75% case fatality at 5 years). Overall, the adjusted risk of dying within one year in the period 1986 to 1989 was 2.22-fold greater (OR 95% CI, 1.27 to 3.85) than in 1998 to 2001 (P<0.001). The greatest falls in one year case fatality were seen in those with Connective PAH (18-fold increased risk of dying in 1986 to 1989 versus 1998 to 2001: P=0.013). Similarly, women (adjusted OR 1.38, 95% CI 1.16 to 1.63: P<0.001) and the most deprived individuals (OR 2.38, 95% CI 1.17 to 4.82: P<0.05) were at greater risk of dying within 5 years. Alternatively, those patients discharged in 1997 were less likely to die during this period compared to their 1986 counterparts, although this difference did not quite reach statistical significance (OR 0.45, 95% CI 0.22 to 1.06: P=0.056). CONCLUSION: This population-based study has confirmed the deadly impact of the three most common forms of PAH. Overall, there are encouraging trends in relation to one and five year adjusted survival rates; particularly in relation to PAH related to connective tissue disorders.