To gain a better understanding of bacterial responses to complex and hostile environments generated within the neutrophil phagosome, we estimated mRNA abundance, using genomic arrays, in Escherichia coli cells ingested by normal and phagocyte oxidase-deficient human neutrophils. Genes regulated by the oxidant sensing transcription factor OxyR were among those strongly induced upon phagocytosis by normal, but not oxidase-deficient, neutrophils. Several genes related to nitrogen metabolism, especially those regulated by the NtrC and NAC proteins and transcribed via the ς⁵⁴ alternative sigma factor, were suppressed by both normal and oxidase-deficient neutrophils. A ΔoxyRS mutant strain of E. coli was significantly more susceptible than the parent strain to neutrophil-mediated killing, which suggests that OxyR-regulated gene products contribute a measure of resistance to neutrophil antimicrobial systems. The hypersusceptibility of the ΔoxyRS mutant was attenuated when oxidase-deficient neutrophils were employed, suggesting that much of the protection afforded by the OxyR regulon is against oxidative antimicrobial factors. Expression profiling of phagocytosed bacteria appears to provide useful information about conditions in the phagocytic vacuole and about bacterial defenses mounted in response to this hostile environment.