[Background] It is expected that thrombus density and perviousness measurements are dependent on CT slice thickness, because density values are blurred in thicker slices. This study quantifies the effect of slice thickness on thrombus density and perviousness measurements. [Methods] Thrombus density and perviousness measurements were performed in 50 patients for varying slice thicknesses, using a manual and semi-automated technique. Linear regression was performed to determine the dependence of density measurements on slice thickness. Paired t-tests were used to test for differences in density and perviousness measures for varying slice thickness. [Results] Thrombus density decreased for increasing slice thickness with approximately 2HU per mm. Perviousness measurements were significantly higher for thick slice compared to thin slice NCCT. [Conclusion] Thick slice NCCT scans result in an underestimation of thrombus density and overestimation of thrombus perviousness.