Objective: To compare the thickness and organization of surface epithelium, and high endothelial venules in subepithelial compartments of human nasopharyngeal and palatine tonsils, with reference to functional differences. Study Design: Comparative cross-sectional. Place and Duration of Study: The Anatomy Department of CPSP Regional Centre, Islamabad, from January to December 2005. Methodology: Thirty samples each of human nasopharyngeal, right palatine and left palatine tonsils were collected by convenience sampling technique. Haematoxylin and eosin stained paraffin sections were examined for surface epithelium. Thickness of stratified squamous and pseudostratified ciliated columnar epithelium was measured, while organization was observed in case of stratified squamous. The high endothelial venules in subepithelial lymphoid compartments were counted. Results: The surface epithelium of nasopharyngeal tonsils (stratified squamous and pseudostratified columnar inclusive) was 63.21+1.93 µm, and that of palatine (stratified squamous) was 143.99+5.94 µm thick (p