Early neurological deterioration (END) affects 20-30% of patients with lacunar stroke within 48h despite optimal treatment. Previously established markers included infection and infarct location on imaging. We studied the utility of measuring global cerebral blood flow (gCBF) measured by CT-Perfusion (CTP) as an early predictor of END in patients with lacunar strokes. 162 patients with lacunar stroke were measured for gCBF including both cerebral hemispheres and cerebellum. We stratified patients by normal gCBF (> 40ml/100mg/min) vs. low gCBF (< 40ml/100mg/min). Stroke location, vascular risk factors, age and gender were assessed. The primary outcome was the change in the NIHSS score after 48h from index stroke. Mean gCBF of the overall cohort was 37.72ml/100mg/min. Both groups had a baseline NIHSS score of 4.2 with similar standard deviations. The NIHSS score decreased by 1.3 points in normal gCBF group and increased by 1.1 points in the low gCBF group. All stroke sites deteriorated in the low gCBF group, particularly the capsula interna, corona radiata, and lateral pontine area. END occurred in 37.8% in low gCBF compared to 3.1% in the normal gCBF patients. In contrast, clinical improvement after 48h occurred in 64.2% of patients with normal gCBF but only 6.1% with low gCBF. Our study supports measurement of gCBF by CTP as a potential imaging biomarker for END. Additionally, it adds evidence to the body of supporting the vulnerability of capsula interna and pontine infarctions to END.