The aim of this study was to assess the ability of self-assembling peptide (P11-4) diffusion, assembly, and remineralization to effect artificial secondary caries-like lesions in human primary teeth in vitro. Enamel-dentin blocks obtained from extracted human primary molars were embedded into epoxy resin blocks. Cavities (approximately 1 x 1 x 2 mm) were prepared on the surface using a high-speed diamond bur under constant water cooling and filled with composite restorative material (Filtek Z250; 3 M ESPE). The samples were immersed in demineralizing solution (20 ml) for 96 h to produce secondary caries lesions and divided into two groups according to the testing materials: fluoride varnish (Duraphat; Colgate, UK) and P11-4 (Curodont Repair; Credentis, Switzerland). Except for the control areas, all samples were remineralized for 3-5 min using the remineralizing agents, and then all the sections were placed in a pH-cycling system for 5 days at 35 degrees C. The pH cycling procedure was followed by micro-CT analysis for the qualitative evaluation of surface changes. The Mann-Whitney U test was used to compare two independent groups. In the comparison of more than two dependent groups, Bonferroni smoothed pairwise analyses were used to determine the source of the Kruskal-Wallis H test difference. The results of the study revealed that the remineralization depths of the peptide group were higher than those of the fluoride group (p < .01). There was a statistically significant difference in remineralization effects between the fluoride and peptide groups. P11-4 can be considered as an effective remineralizing agent for secondary caries lesions.