Sickle cell disease (SCD) is a chronic disease with a significant rate of neurological complications in the first decade of life. In this retrospective study, cortical thickness was examined in children with SCD who had no detectable abnormalities on conventional magnetic resonance imaging/magnetic resonance angiography. Regional differences in cortical thickness from SCD were explored using age-matched healthy controls as comparison. A comparison analysis was done for SCD (n = 28) and controls (n = 29) based on age (5-11; 12-21 years), due to the age-dependent variation in cortex maturation. Distinct regions of thinning were found in SCD patients in both age groups. The number, spatial extent, and significance (P < 0.001) of these areas of thinning were increased in the older SCD group. Regions of interest (ROIs) were defined on the areas of highly significant thinning in the older group and then mapped onto the younger cohort; a multiparametric linear regression analysis of the ROI data demonstrated significant (P < 0.001) cortical thinning in SCD subjects, with the largest regions of thinning in the precuneus and the posterior cingulate. The regionally specific differences suggest that cortical thickness may serve as a marker for silent insults in SCD and hence may be a useful tool for identifying SCD patients at risk for neurological sequelae.