In vivo regulation of matrix vesicles (MV) during primary bone formation was examined using tibial marrow ablation in rats as the experimental model. The effects of bone-bonding and nonbonding implants on the number of MV/μm2 of matrix and the alkaline phosphatase (ALPase) and phospholipase A2 (PA2) activities of MV-enriched microsomes (MVEM) isolated from the healing bone were studied. MV concentration, ALPase, and PA2 were increased by bone-bonding implants by day 3 post-surgery; a similar effect was seen in the contralateral limb, but at a lower magnitude. Nonbonding implants had no effect at day 3 and decreased MV concentration and PA2 activity at later time points; the same behavior was observed in the contralateral limb. These results demonstrate that MVs are influenced in a differential manner by implant materials, both locally and systemically, and can be regulated during primary mineralization.