Introduction: Molar Incisor Hypomineralisation (MIH) is a qualitative defect of enamel which is more prone to posteruptive enamel breakdown resulting in the early invasion of dental caries compared to a normal enamel tooth structure. Aim: To assess the differences in the enamel permeability of permanent teeth with and without MIH using Scanning Electron Microscopy. Materials and Methods: Out of the sixteen children, eight children with and eight without MIH were randomly selected. Fully erupted maxillary anterior teeth were subjected for evaluation in this study. Vinyl Polysiloxane impression material was used to make impressions for SEM evaluation. The teeth surfaces were divided, into 9 different morphological areas for assessment. Negative replicas representing enamel droplets were assessed. Odd's ratio was calculated by Logistic Regression Analysis. Results: Presence of enamel droplets was noticed in both the groups, more predominantly in teeth with MIH. On comparing the individual regions, presence of enamel droplets in the hypomineralised areas had significant difference compared to normal enamel, with p-value 0.0012, which was statistically significant, with an odds ratio of 3.4. Conclusion: This study demonstrated a high presence of droplets in MIH teeth compared to teeth without MIH, suggesting a possible high enamel permeability which in turn can be a predisposing factor for dental caries in teeth with MIH.