Objectives: To investigate the relationship of gap size and secondary caries in a newly developed secondary caries microbial model that permits adjustment of the gap between the tooth and a restoration. Methods: Tooth-resin-matrix composite specimens were mounted on gap-model stages with a gap size of 50 or 500 µm in experiment 1, and 0, 25, 250, or 1,000 µm in experiment 2. They were attached to plastic Petri plates, gas-sterilized and then incubated in a microbial caries model (with Streptococcus mutans TH16 in 1% sucrose tryptic soy broth for 1 h, 4 times/day, and with a buffer solution for the rest of the day). After 8 days of incubation, tooth specimens were sectioned and stained overnight with a rhodamine B solution. Digital images taken under a confocal microscope were analyzed for lesion size at the outer surface lesion and wall lesion (WL). Results: Gap size was found to affect the development of dentin WL area in experiment 1 and enamel and dentin WL areas in experiment 2, with bigger lesions being observed in the wider gap group (p < 0.05). Conclusion: The findings of this study suggest that the size of the gap between tooth and restoration affects the development of secondary caries along the cavity wall.