BACKGROUND: HIV and SIV infections induce NK cell dysfunction and hematopoietic defects in the bone marrow, but the effects of infection on bone marrow NK cell development and function are unknown. METHODS: Bone marrow NK cells were analyzed from both nave and chronically SIV-infected rhesus macaques using polychromatic flow cytometry. RESULTS: NK cell frequencies were reduced in infected compared with nave animals, associated with increased apoptosis. Bone marrow NK cells from SIV-infected macaques upregulated perforin expression, suggesting increased cytotoxicity, and shifted toward a more mature CD16(+) NK cell subpopulation phenotype. Unexpectedly, expression of the trafficking markers 47, CCR7, and CD62L was unchanged on bone marrow NK cells during SIV infection. CONCLUSION: These data demonstrate that during SIV infection, bone marrow NK cells are reduced in number, but upregulate cytotoxic functions. Furthermore, our data suggest acquired cytotoxicity and loss may be due to in situ NK cell differentiation and not emigration.