Aim: Recent advances including the incorporation of antibacterial substances, such as chlorhexidine, into restorative materials such as glass ionomer cement (GIC), might alter the physical properties of the material, which might affect the marginal seal of the restorations. Hence, the objective of this study was to compare the marginal sealing ability of GC Fuji IX modified with 1% chlorhexidine diacetate and conventional GC Fuji IX. Materials and methods: Sixty healthy molars were selected from the oral cavities of 30 children. The teeth were divided into two groups: Group I, teeth restored with 1% chlorhexidine diacetate modified GC Fuji IX and group II, teeth restored with GC Fuji IX. The restored teeth were extracted following 4 weeks and immersed in 2% basic fuchsin solution for 24 hours. They were then sectioned and scored under a light microscope of 10 × 10 magnification for dye penetration. Results: On statistical analysis difference between Chlorhexidine-Modified GIC group and GIC group with regard to grade of microleakage was found to be statistically nonsignificant (p = 0.543). Conclusion: Since, addition of 1% chlorhexidine diacetate to GC Fuji IX showed comparable results with regard to microleakage, it can be considered a valuable alternative especially in atraumatic restorative treatment and for general clinical utility in restorative dentistry.