The objective of this paper was to analyse sex differences of the thickness of the subchondral mineralised tissue zone (SMZ), and to find out whether systematic changes of SMZ thickness are associated with naturally occurring, non-full-thickness cartilage lesions of human patellae. In 32 methyl-methacrylate-embedded specimens (16 normal, 8 with focal medial, and 8 with lateral lesions) the SMZ thickness was determined, using a binocular macroscope and an image analysing system. In each case, the thickness distribution was reconstructed throughout the entire joint surface. The maximal and mean SMZ thicknesses were significantly higher in males than in females (P < 0.01). In normal patellae and those with lateral lesions, the thickness was significantly thicker laterally than medially (P < 0.05), but it was not in specimens with medial damage. Patellae with medial damage exhibited a significantly lower total mean and lateral mean (P < 0.05). A lower SMZ thickness was found directly beneath medial lesions than beneath lateral ones, but the local thickness was always in the range of that observed in normal specimens. We conclude that differences of patellar SMZ thickness exist between males and females. Naturally occurring cartilage lesions appear, however, not to be associated with local changes of SMZ thickness, but they may be associated with an altered regional distribution pattern within the joint surface.