It is important to predict progressive deficit (PD) in isolated pontine infarction, a relatively common problem of clinical stroke practice. Traditionally, lacunar infarctions are known with their progressive course. However, few studies have analyzed the branch atheromatous disease subtype as a subtype of lacunar infarction, separately. There are also conflicting results regarding the relationship with the topography of lesion and PD. In this study, we classified etiological subtypes and lesion topography in isolated pontine infarction and aimed to investigate the association of etiological subtypes, lesion topography and clinical outcome with PD. We analyzed demographics, laboratory parameters, and risk factors of 120 patients having isolated pontine infarction and admitted within 24 h retrospectively. PD was defined as an increase in the National Institutes of Health Stroke scale >= 2 units in 5 days after onset. Patients were classified as following: large artery disease (LAA), basilar artery branch disease (BABD) and small vessel disease (SVD). Upper, middle and lower pontine infarcts were identified longitudinally. Functional outcome at 3 months was determined according to modified Rankin scores. Of 120 patients, 41.7% of the patients were classified as BABD, 30.8% as SVD and 27.5% as LAA. 23 patients (19.2%) exhibited PD. PD was significantly more frequent in patient with BABD (p 0.006). PD was numerically higher in patients with lower pontine infarction. PD was associated with BABD and poor functional outcome. It is important to discriminate the BABD neuroradiologically from other stroke subtypes to predict PD which is associated with poor functional outcome in patients with isolated pontine infarctions.