Background and purpose Isolated pontine strokes cause characteristic neurological syndromes and have a good short-term prognosis. The aim of this study was to examine the long-term survival, cumulative recurrence rate and clinical handicap of patients with isolated pontine infarcts of different aetiology. Methods One hundred consecutive patients with an isolated pontine infarction were identified by imaging studies and evaluated prospectively. After extensive study, cases were classified according to the aetiopathogenetic mechanisms: stroke due to basilar artery branch disease (BABD), small-artery disease ( SAD) and large-artery-occlusive disease (LAOD). During a mean follow-up period of 46 months, stroke presentation and initial course, early and long-term mortality, disability and recurrence were evaluated. Results BABD was the most frequent cause of isolated pontine ischaemia (43%), followed by SAD (34%) and LAOD (21%). Hypertension was the most prominent risk factor, especially among patients with SAD (94.1%). Neurological impairment on admission was more severe in the LAOD group, followed by BABD. After 1 month patients with LAOD had the highest cumulative mortality (14.3%, p= 0.026) and more severe disability (61.1%, p= 0.001). Five-year mortality rate was 20.6%, 14% and 23.8% in the SAD-, BABD- and in LAOD-group respectively ( p= 0.776). Cumulative 5-year recurrence rate was 2.3% for BABD, 14.3% for LAOD, and 29.4% for SAD ( p= 0.011). Conclusions Overall long-term survival of patients with isolated pontine infarcts is good. Initial differences regarding short-term outcome in infarctions of different aetiology resolve with time. Effective secondary prevention among SAD patients may limit stroke recurrence and positively influence long-term prognosis.