Jdp2 is an AP-1 family transcription factor that regulates the epigenetic status of histones. Previous in vitro studies revealed that Jdp2 is involved in osteoclastogenesis. However, the roles of Jdp2 in vivo and its pleiotropic functions are largely unknown. Here we generated Jdp2–/– mice and discovered its crucial roles not only in bone metabolism but also in differentiation of neutrophils. Jdp2–/– mice exhibited osteopetrosis resulting from impaired osteoclastogenesis. Jdp2–/– neutrophils were morphologically normal but had impaired surface expression of Ly6G, bactericidal function, and apoptosis. We also found that ATF3 was an inhibitor of neutrophil differentiation and that Jdp2 directly suppresses its expression via inhibition of histone acetylation. Strikingly, Jdp2–/– mice were highly susceptible to Staphylococcus aureus and Candida albicans infection. Thus, Jdp2 plays pivotal roles in in vivo bone homeostasis and host defense by regulating osteoclast and neutrophil differentiation. ► Jdp2–/– mice exhibit osteopetrosis resulting from impaired osteoclastogenesis ► Jdp2–/– neutrophils exhibit impaired Ly6G, apoptosis, and bactericidal function ► ATF3 inhibits neutrophil differentiation and is suppressed by Jdp2 ► Jdp2–/– mice are highly susceptible to bacterial and fungal infection