Early childhood caries (ECC) is a serious problem that progresses rapidly and often goes untreated. Current traumatic treatments may be replaced by safe and effective remineralization at very early stages. ObjectiveThe aim of this in vitro study was to evaluate the remineralization effects of casein phosphopeptide–amorphous calcium phosphate (CPP–ACP) paste on enamel lesions by assessing ultrastructure, nanomechanical properties, and compound and elemental analysis. MethodsEnamel specimens from 6-year-old children were divided into groups: (1) native enamel; (2) water as negative control; (3) 500ppm NaF as positive control; and (4–7) CPP–ACP paste for 4, 8, 12, and 24h, as test groups. Ultrastructure and roughness were observed by atomic force microscopy (AFM); nanohardness and elastic modulus were measured by nanoindentation; compound and crystal size of enamel surface patterns were investigated by X-ray diffractometer (XRD). An electron microprobe (EPMA) was used for element analysis. Data were analyzed using one-way ANOVA. ResultsThe CPP–ACP paste repaired the microstructure of enamel, including prism and interprism, through significantly increased hydroxyapatite crystal size (12.06±0.21nm) and Ca/P molar ratios (1.637±0.096) as compared with NaF (8.56±0.13nm crystal size and 1.397±0.086 Ca/P, p<0.01). Both CPP–ACP and NaF decrease roughness, and increase the nanohardness and elastic modulus, with no significant differences between the materials. ConclusionsThe CPP–ACP paste is more suitable for children than NaF, due to advantages for remineralization. The AFM, nanoindentation, EPMA, and XRD are very helpful methods for further understanding of microscale and nanoscale remineralization mechanisms.