Objectives The aim of this study was to investigate the effects of polymerization contraction, shrinkage stress and Young's modulus of nanofiller containing resin composites on early marginal adaptation of restorations in cavities. Methods Six nanofiller containing and two reference resin composites were studied. Marginal gap widths of restorations in cylindrical 4.2 mm wide and 1.5 mm deep dentin cavities, non-bonded or bonded with a self-etch adhesive, and in Teflon cavities of same dimensions were determined 15 min after irradiation ( n = 8). Polymerization shrinkage strains were measured using the bonded-disk ( n = 8) and a strain gage method ( n = 8). For determination of contraction stress the composites ( n = 10) were bonded to and cured in Araldit molds using a photoelastic method. Flexural moduli of the restoratives were studied according to ISO specification 4049 ( n = 5). Statistical analysis was performed with one- and two-way ANOVA, Kruskal–Wallis ANOVA test and post hoc tests ( p < 0.05). Results Only two nanofiller composites (Kalore, GC, Japan) and Venus Diamond (Heraeus Kulzer, Germany) showed consistently gap-free margins in bonded dentin cavities. The mean gap widths in non-bonded and in Teflon cavities were 6.1–12.8 and 14.1–25.5 μm, and linearly correlated ( r 2 < 0.85). Significant linear relationships were observed between strain, stress and marginal gap widths in non-bonded and Teflon cavities ( p < 0.01). Flexural moduli (15 min) were between 1.66 and 8.63 GPa. Significance Marginal cavity adaptation of restorations in bonded dentin cavities reflects complex interactions between adhesive bonding on the one hand, and polymerization contraction strain, stress and elastic modulus, on the other.