Tooth enamel is the stiffest tissue in the human body with a well-organized microstructure. Developmental diseases, such as enamel hypomineralisation, have been reported to cause marked reduction in the elastic modulus of enamel and consequently impair dental function. We produce evidence, using site-specific transmission electron microscopy (TEM), of difference in microstructure between sound and hypomineralised enamel. Built upon that, we develop a mechanical model to explore the relationship of the elastic modulus of the mineral-protein composite structure of enamel with the thickness of protein layers and the direction of mechanical loading. We conclude that when subject to complex mechanical loading conditions, sound enamel exhibits consistently high stiffness, which is essential for dental function. A marked decrease in stiffness of hypomineralised enamel is caused primarily by an increase in the thickness of protein layers between apatite crystals and to a lesser extent by an increase in the effective crystal orientation angle.