Accurate segmentation of ventricular cerebrospinal fluid (CSF) regions in stroke CT images is important in assessing stroke patients. Manual segmentation is subjective, time consuming and error prone. There are currently no methods dedicated to extracting ventricular CSF regions in stroke CT images. 102 ischemic stroke CT scans (slice thickness between 3 and 6 mm, voxel size in the axial plane between 0.390 and 0.498 mm) were acquired. An automated template-based algorithm is proposed to extract ventricular CSF regions which accounts for the presence of ischemic infarct regions, image noise, and variations in orientation. First, template VT₂ is registered to the scan using landmark-based piecewise linear scaling and then template VT₁ is used to further refine the registration by partial segmentation of the fourth ventricle. A region of interest (ROI) is found using the registered VT₂. Automated thresholding is then applied to the ROI and the artifacts are removed in the final phase. Sensitivity, dice similarity coefficient, volume error, conformity and sensibility of segmentation results were 0.74 ± 0.12, 0.8 ± 0.09, 0.16 ± 0.11, 0.45 ± 0.39, 0.88 ± 0.09, respectively. The processing time for a 512 × 512 × 30 CT scan takes less than 30 s on a 2.49 GHz dual core processor PC with 4 GB RAM. Experiments with clinical stroke CT scans showed that the proposed algorithm can generate acceptable results in the presence of noise, size variations and orientation differences of ventricular systems and in the presence of ischemic infarcts.