The interdisciplinary field called osteoimmunology has attracted much attention, due to the observations that bone destruction is caused by an abnormal activation of the immune system in rheumatoid arthritis, and mice lacking immunomodulatory molecules often exhibit an unexpected bone phenotype. Osteoclasts are cells of monocyte/macrophage origin that degrade the bone matrix in health and disease. Receptor activator of NF-kappaB ligand (RANKL), a tumor necrosis factor (TNF) family cytokine, is an essential osteoclastogenic factor linking the bone and the immune system. In the genomewide screening of RANKL-inducible genes using GeneChip, we identified nuclear factor of activated T cells c1 (NFATc1) as the master transcription factor for osteoclastogenesis. We also applied the GeneChip method to the analysis of osteoimmunological regulation: analysis of costimulatory signal for RANKL and the target genes of antirheumatic drugs. Here we summarize our recent findings in the field of osteoimmunology obtained by GeneChip.