Background: Titanium (Ti) implants are extensively used in reconstructive surgery and orthopedics. However, the intrinsic inertness of untreated Ti implants usually results in insufficient osseointegration. In order to improve the osteoconductivity properties of the implants, they are coated with hierarchical microtopographic/nanotopographic coatings employing the method of molecular layering of atomic layer deposition (ML-ALD). Results: The analysis of the fabricated nanostructured relief employing scanning electron microscopy, atomic force microscopy, and electron spectroscopy for chemical analysis clearly demonstrated the formation of the nanotopographic (<100 nm) and microtopographic (0.1-0.5 µm) titano-organic structures on the surface of the nanograined Ti implants. Subsequent coincubation of the MC3T3-E1 mouse osteoblasts on the microtopographic/nanotopographic surface of the implants resulted in enhanced osteogenic cell differentiation (the production of alkaline phosphatase, osteopontin, and osteocalcin). In vivo assessment of the osseointegrative properties of the microtopographically/nanotopographically coated implants in a model of below-knee amputation in New Zealand rabbits demonstrated enhanced new bone formation in the zone of the bone-implant contact (as measured by X-ray study) and increased osseointegration strength (removal torque measurements). Conclusion: The fabrication of the hierarchical microtopographic/nanotopographic coatings on the nanograined Ti implants significantly improves the osseointegrative properties of the intraosseous Ti implants. This effect could be employed in both translational and clinical studies in orthopedic and reconstructive surgery.