This invivo study was carried out to evaluate the effect of nanohydroxyapatite (n-HAp); applied with or without prior application of chlorhexidine (CHX), on remineralization of caries-affected and caries infected dentine types. Forty molars in eight patients having class I caries and no pulpal involvement were selected. In each selected molar, caries was removed except from the pulpal floor. Thereafter, molars were divided into two groups (n= 20) according to the type of carious dentine left on the pulpal floor; caries-affected or infected dentine. Each group was further subdivided into two subgroups (n=10) according to the material that was applied on carious dentine; n-HAp with or without 2% CHX. All cavities were finally sealed with glass ionomer restoration. Assessment of mineral density was performed at base line, one and three months using digitized radiography. The results showed increased mineral density in caries-affected dentine group; with no significant difference neither n-HAp was applied with or without CHX, nor was the application time increased more than one month. In caries-infected dentine group, however, mineral density was decreased. Such decrease was significantly evident at the third month; when n-HAp was applied without CHX. It was concluded that n-HAp could only promote remineralization of cariesaffected dentine. Additionally, although application of CHX prior to n-HAp showed no considerable influence on remineralization, yet, it could be recommended in case of caries-infected dentine as an antiseptic.