This in vivo study was conducted to compare and evaluate the microleakage of two modified glass ionomer cements on deciduous molars. Thirty children (10-16 years) were selected. In each patient, standardized class V cavities were prepared on the buccal surfaces of two different retained deciduous molars and these cavities were restored with GC Fuji II LC (Improved) and GC Fuji IX GP, respectively. Following a period of four weeks after the restoration, these teeth were extracted and immersed in 2% Basic Fuschin dye solution for 24 hours. The depth of dye penetration was assessed after sectioning the teeth and the microleakage determined. The results were statistically analyzed using Student 't' test. It was concluded that both the materials, GC Fuji II LC (Improved) and GC Fuji IX GP were comparable in performance and can be considered to be materials safe for Pedodontics usage, and decrease bacterial penetration.