To identify proteins implicated in peripheral nerve regeneration, we performed two-dimensional polyacrylamide gel electrophoresis and subsequent mass spectrometry analysis using nerve-injured hypoglossal nuclei of rat. We have identified annexin III (ANX III/ANX A3) as an induced protein after rat hypoglossal nerve injury. ANX III is known as a Ca2+-dependent phospholipid-binding protein, but its physiological function is mostly unknown. By in situ hybridization and immunohistochemistry, we demonstrated that ANX III expression was induced specifically in activated (axotomy-stimulated) microglia after nerve injury. ANX III was the most prominent ANX expressed in microglia of the major ANX family members (ANX I-VI). Hybridization signals for other ANX mRNAs (II, IV, V, and VI) were mainly observed in neuronal cells, and no significant hybridization signal for ANX I mRNA was detected in hypoglossal nuclei. In cultured microglia, ATP treatment induced ANX III translocation to the ruffling membrane where F-actin was accumulated. Further in vitro studies revealed that ANX III was not secreted and had F-actin binding activity in a Ca2+-dependent manner. These results suggest that ANX III may be a Ca2+-dependent mediator between phospholipids and F-actin in microglia stimulated by peripheral nerve injury. © 2006 Wiley-Liss, Inc.