This in vitro study aimed to evaluate the internal adaptation of two different self-adhering flowable composite resin materials used as liners under Class II restorations using microcomputed tomography (micro-CT) analysis. Standard box-only cavities were prepared in 30 extracted human third molar teeth. The cervical floor of the proximal box was 1 mm below the cementoenamel junction. After the preparations were completed, the teeth were randomly and equally divided into three groups based on the type of liner used: group 1, universal flowable composite (control; CO); group 2, self-adhering flowable composite (Fusio Liquid Dentin; FU); and group 3, self-adhering flowable composite (Vertise Flow; VE). After lining, the cavities were restored using 2-mm increments of the nanohybrid composite. After storing the specimens for 24 h in distilled water at 37 degrees C, all teeth were subjected to 5000 thermal cycles of 5/55 degrees C. Subsequently, the teeth were immersed in a 50% silver nitrate dye at 23 degrees C for 4 h. Following the immersion, high-resolution micro-CT images were obtained. Silver nitrate penetration into the microgap between the tooth and restoration was calculated for each specimen as a percentage of the entire length of the pulpal floor using image analysis software. One-way analysis of variance was performed to compare the differences among the groups (p = 0.05). No significant differences were observed between the control and self-adhering composite groups (FU, VE; p > 0.05). The performance of self-adhering composites was similar to that of universal flowable composites in terms of marginal microleakage.