The disassembly of apoptotic cells into apoptotic bodies (ApoBDs) is essential for the efficient clearance of apoptotic debris by phagocytes. Defects in this process can lead to the release of pro-inflammatory molecules and consequently, trigger the onset of inflammatory diseases. Currently, the only known regulators of apoptotic cell disassembly are intrinsic factors such as rho-associated kinase 1, Pannexin 1 and Plexin B2. However, whether cell extrinsic factors also contribute to this process is yet to be defined. To investigate this, developmental and drug-induced apoptosis in secAnnexins5:mVenus zebrafish embryos (which secrete fluorescently-tagged Annexin V allowing definitive tracking of cell death) was monitored by time-lapse imaging, 24 hours post fertilisation. Qualitative analysis by confocal microscopy demonstrated global apoptosis in both models, and in vivoapoptotic cell disassembly was evident by the significant production and accumulation of ApoBDs. Similarly, quantitative analysis of C57bl/6 mice treated with either dexamethasone or X-ray irradiation also revealed substantial CD4+/CD8+thymic ApoBD formation in vivo, as well as a large number of CD11b+/CD68+/F4/80+macrophages within the thymus. In contrast, ex vivoinduction of thymic apoptosis significantly reduced both the levels of thymic-ApoBD formation and the number of macrophages, suggesting a correlation between ApoBD formation and macrophage infiltration to the site of death. Collectively, this data demonstrates that the disassembly of apoptotic cells is a highly efficient in vivophenomenon, potentially increased by extrinsic factors such as recruited phagocytes.