Objectives: This in vitro study was carried out to assess the microtensile bond strength of resin composite to pretreated dentin by hydroxyapatite nanoparticles at two time interval (24hours and 3months). Methods: Nano-rods hydroxyapatite nanoparticles (HA NPs) were added by conc. of 2% and 10% to ethanol solution, selected adhesive system was modified by mixing it with 2% wt HA NPs. Occlusal dentin surface of 80 sound human molar teeth were prepared to expose a flat dentin surface at level 0.5mm below the dentino-enamel junction. The specimens were divided into four groups according to the bonding protocol either: No pre-treatment by hydroxyapatite nanoparticles (A1), application of HA NPs at 2% (A2) and 10% (A3) conc. on the etched dentin before adhesive application (Adper Single Bond 2) and application of the adhesive that was modified by adding of HA NPs at 2%wt (A4) to it. Adhesive system was light cured and followed by building-up of nano-filled resin composite (Filtek Z350 XT). Each specimen was sectioned to produce sticks of 1.0 mm2 central sticks were selected for the test. Two represented beams of each group were selected for ultra-morphological examination by using Environmental Scanning Electron Microscope. Results: A1 and A3 after 3 months showed a significant reduction in the mean microtensile bond strength compared to 24 hours aging period (p=0.013), while A2 and A4 after 3 months showed a non- significant reduction in the mean microtensile bond strength compared to 24 hours aging period (p=0.628). Conclusion: Modifying the adhesive system by 2% wt HA NPs did not hinder bonding of resin composite to dentin and produced adhesive system that is less prone to degradation, while 10% conc. of HA NPs antagonized penetration of resin tags into dentinal tubules and formation of hybrid layer.