INTRODUCTION: Fluoride containing casein phosphopeptide amorphous calcium phosphate (CPP-ACP) varnishes are now available as (MI Varnish). It has an effect on the remineralization process of demineralized enamel, since it has the highest release of calcium and fluoride ions. OBJECTIVES: To study the remineralizing effect of fluoride varnish containing casein phosphopeptide amorphous calcium phosphate (MI varnish) on the remineralization of caries-like lesions in primary teeth compared to sodium fluoride varnish. MATERIALS AND METHODS: Twenty-four freshly extracted primary maxillary incisors with standardized 4x4 windows were immersed in demineralizing solution for four days. Teeth were divided into two groups, group I (n=12 teeth); MI varnish and group II (n=12 teeth); Prevident varnish. They were sectioned into two halves in a buccolingual direction (48 specimens). One half was treated with the remineralizing agent and the other half remained untreated and served as its control. Specimens were assigned into subgroup I A (MI varnish) n=12 specimens, subgroup I B (untreated) n=12 specimens, subgroup II A (Prevident varnish) n=12 specimens and subgroup II B (untreated) n=12 specimens. Specimens were subjected to pH cycling for ten days. The specimens were evaluated quantitatively using energy dispersive x-ray spectrometer (EDX). RESULTS: MI varnish treated specimens (subgroup I A) showed significant high mean Ca, Ca/P ratio than the untreated specimens. Also, Prevident varnish treated specimens showed significant high mean Ca, Ca/P ratio than the untreated specimens. Median percent change of Ca/P ratio of MI varnish treated specimens was significantly higher than Prevident varnish treated specimens. CONCLUSIONS: Fluoride varnish containing CPP-ACP has a higher remineralization potential of the caries-like lesion in primary teeth in comparison to sodium fluoride varnish.