Microparticulate systems have attracted a great deal of attention over the past few years as a carrier for the delivery of cells and proteins in the treatment of defective tissues. The composition of microparticulates is regarded as being of utmost importance for the successful recruitment of the cells involved in the tissue regeneration process. Collagen-apatite nanocomposites mimicking the extracellular bone matrix are thus considered to be a potential vector for bone regeneration, either directly or through the delivery of osteogenic cells. In this study, we developed microspheres constituted of collagen and apatite for the treatment of skeletal defects. The apatite-precipitated collagen solution (30% apatite) was formed into microspheres under a water-in-oil emulsion condition. Spherical particles with diameters of tens to hundreds of micrometers (average of approximately 166 microm) were successfully produced. The internal structure of the microspheres featured a typical nanocomposite wherein apatite nanocrystalline precipitates were organized evenly within the reconstituted collagen matrix. The nanocomposite microspheres were observed to recruit favorable adhesion and growth of rat bone marrow derived stem cells. The cells supported on the nanocomposite microspheres stimulated the expression of a series of bone-associated genes. The osteogenic marker, alkaline phosphatase, was secreted to a significantly higher level on the nanocomposite microspheres than on the pure collagen counterpart. The present finding suggests that the collagen-apatite nanocomposite microspheres have high osteogenic potential and are useful for tissue-engineering applications.