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Microsporidia continue to cause opportunistic enteric and systemic infections in immune-compromised individuals worldwide and also cause persistent infections in otherwise healthy mammalian hosts. Macrophages can be activated during innate and adaptive immune responses to kill intracellular microsporidia yet some organisms escape to continue infection. Earlier studies by others demonstrated that Encephalitozoon spp. inhibited apoptosis in non-phagocytic host cells, and the purpose of this study was to determine if microsporidia can also inhibit apoptosis in phagocytic cells such as macrophages. THP1-differentiated macrophages infected with live Encephalitozoon cuniculi or Vittaforma corneae inhibited staurosporine-induced apoptosis three days later as determined by lower levels of TUNEL staining and caspase 3 activity compared with uninfected control macrophages induced with staurosporine. Conversely, THP1 macrophages incubated with dead microsporidia and treated with staurosporine three days later exhibited significantly higher levels of apoptosis than THP1 macrophages treated only with staurosporine. PCR apoptosis pathway micro-array analysis corroborated these bioassay findings. Anti-apoptosis genes including BLC2 and TP53 were significantly up-regulated in macrophages infected with microsporidia for three days while pro-apoptosis genes such as FADD, CASP3, CD40LG, LTA, and several TNF-family genes were up-regulated in the macrophages incubated with dead organisms. Interestingly, the inhibition of apoptosis was more pronounced with E. cuniculi, which replicates within parasitophorous vacuoles, than V. corneae, which replicates in close association with endoplasmic reticulum in the cytoplasm. These results open the door to consider targeting apoptosis pathways for controlling microsporidia infections. [Supported by a Tulane Research Enhancement Fund grant and national primate research center support from NIH via Grant OD011104.]