Background: Caries detector dyes are introduced to aid in identifying infected dentine. Many researchers claim that they are not specific in identifying infected dentine since dyes also stains sound tooth surfaces. The use of a dentine bonding agent could help in avoiding the penetration of caries detector dyes to some extent in less mineralized primary teeth. This study assesses caries detector dyes penetration in primary teeth with or without dentine bonding agent application. Methodology: Ninety primary extracted carious teeth were considered for the study. Teeth were divided in to two groups (45 teeth each group): group I with dye application without dentine bonding agent and group II with dye application after dentine bonding agent; in both groups three different types of dyes were used. All cavity walls and surfaces of samples in group 1 were stained with caries detector dyes for 10 s, subsequently washed with water for another 10 s and finally air-dried. A similar procedure was carried for teeth in group II after the application of a bonding agent on visibly sound tooth surfaces without the use of an etchant. Results: A statistically significant difference between two groups for staining of different tooth surfaces was noted. A Kruskal–Wallis one-way ANOVA revealed a statistically significant difference in stain removal among the different groups either by distilled water or sodium hypochlorite were observed. Conclusion: A dentine bonding agent can help in preventing caries detector dye penetration in noncarious tooth surfaces of deciduous teeth.