Endoreduplication is an alternative cell cycle that omits cell division such that cellular ploidy increases, generating “endopolyploidy”. Endoreduplication is common among eukaryotes and is thought to be important in generalized cell differentiation. Previous research on ants suggests that they endoreduplicate in body segment-dependent manners. In this study, we measured endopolyploidy of specific organs within ant body segments to determine which organs are driving these segment-specific patterns and whether endopolyploidy is related to organ function. We dissected fourteen organs from each of five individuals of Dinoponera australis and measured endopolyploidy of each organ via flow cytometry. Abdominal organs had higher levels of endopolyploidy than organs from the head and thorax, driven by particularly high ploidy levels for organs with digestive or exocrine function. In contrast, organs of the reproductive, muscular, and neural systems had relatively low endopolyploidy. These results provide insight into the segment-specific patterns of endopolyploidy previously reported and into the specific organs that employ endoreduplication in their functional development. Future work aimed at quantifying the metabolic and gene expression effects of endoreduplication will clarify how this often overlooked genomic event contributes to the development and function of specialized organs across the breadth of taxa that are known to endoreduplicate.