Purpose: To evaluate the reliability of marginal leakage assessment of self-etch adhesive Class II resin composite restorations in primary molars prepared in vivo using the micro-CT. Methods: Fourteen primary molars, divided over seven ART and seven traditional resin composite Class II restorations, were subjected to marginal leakage test using a 50% (w/v) silver nitrate solution for 4 hours by a micro-CT. Two evaluators selected the image with the deepest marginal dye penetration for each restoration from the occlusal and approximal surfaces on consensus. The deepest dye penetration depth and total length of the axial cavity wall from both the occlusal and from the approximal surface were measured manually using morphometric quantification software by three evaluators independently. ANOVA was applied to test for differences in marginal leakage scores between the three evaluators. Results: There was no marginal leakage found in five traditional and one ART restoration. The percentage of silver nitrate penetration depth from the cervical-approximal site ranged from 10.2-92.6%. There was only a statistically significant difference observed in measuring total axial wall length from the cervical-approximal site between the three evaluators (P= 0.02). This explanatory investigation showed that the micro-CT was a very useful device for developing a standardized method for measuring marginal leakage from samples obtained in vivo. In combination with 50% (w/v) silver nitrate and 4-hour immersion, marginal leakage along the restoration-tooth tissue interface was accurately and reliably measured. (Am J Dent 2008;21:393-397).