Pulmonary hypertension has a complex pathobiology and the term pulmonary arterial hypertension (PAH) includes a variety of pulmonary hypertensive diseases that have different aetiologies, but which may have a similar clinical presentation and, in some cases, the same response to medical treatment. More recent classifications have been based on aetiology, functional data and clinical presentation, but morphometric studies have shown differences in the distribution and prevalence of vascular changes amongst cases of PAH of different aetiologies. Recent advances in the understanding of some aspects of the genetic and molecular mechanisms, together with detailed descriptions of the histopathological findings in PAH cases of different aetiologies, should contribute to a better understanding of the relationships of the various subsets of the disease, the prognostic implications and possible treatment options.