Aim: This study sought to evaluate the tooth mineral density (TMD) for the different lesion types in hypomineralised first permanent molars (FPMs) and compare them to unaffected enamel in clinically sound FPMs. Design: Eighteen FPMs with varying degrees of hypomineralised enamel were grouped into brown, yellow/creamy and white lesion types. Micro-CT was used to determine the TMD for each lesion type, and for unaffected enamel at different locations in the outer, middle, and inner-third of the enamel. Results: The average TMD for brown, yellow/creamy, white and unaffected enamel was 1.79, 2.21, 2.43 and 2.46 g/cm3, respectively. Brown and yellow/creamy lesions exhibited a statistically significant difference when compared to white lesions and unaffected enamel. However, no statistical difference was evident in TMD between white lesions and unaffected enamel. The TMD increased from the outer-third to inner-third for brown and yellow/creamy lesions (p < 0.05), while in white lesions and unaffected enamel, the TMD decreased from the outer-third to inner-third (p < 0.05). Conclusion: TMD was lowest for brown lesions followed by yellow/creamy lesions while the TMD for white lesions was similar to unaffected enamel.