The balance between myeloid and lymphoid populations must be well controlled especially during pathological condition. In this study, we report that osteopontin (OPN), which is known as a cytokine, skews the balance between myeloid and lymphoid populations during pathological conditions. Importantly, OPN has two isoforms, secreted OPN (sOPN) and intracellular OPN (iOPN). Because OPN has been almost exclusively studied as sOPN, roles of iOPN have been overlooked. Here, using a new iOPN knock-in mice, which express iOPN but not sOPN, we found that the each OPN isoform shifts a balance between myeloid and lymphoid cell populations by selectively controlling apoptosis in a cell type-specific manner: iOPN reduces population sizes of myeloid progenitors and myeloid cells, and sOPN increases population sizes of lymphoid cells. The increase of lymphoid cell populations by sOPN leads to severe T cell-mediated colitis. In contrast, the decrease of myeloid cell populations by iOPN reduced resistance against acute systemic Candida infection. These findings suggest that the two isoforms of OPN cooperatively work to skew the cell population balance towards lymphoid cell populations and modify immune responses during autoimmunity and infection.