Mycobacterium avium subspecies paratuberculosis (MAP) primarily infects subepithelial macrophages in the ileum of susceptible animals. It was hypothesized that like other mycobacterial species, this organism avoids macrophage killing and is able to persist within a modified phagosome. Furthermore, it was hypothesized that survival in the phagosome environment is dependent on the expression of specific virulence factors that allow MAP to prevent phagosome acidification and the arrest of endocytic processing. In this study various techniques were used to assess MAP gene expression during growth in normal laboratory culture conditions and during growth within bovine macrophages. MAP may be required to adapt to limited oxygen availability within the phagosome and also during periods of persistence or dormancy, therefore gene expression following adaptation to hypoxia was also examined. Initially, differential display - reverse transcription PCR (RT-PCR) and specific RT-PCR techniques were used to identify differences in gene expression. The expression of specific targets including, katG, furA, hspX, and an ideR homolog, were examined in all three MAP growth conditions. Subsequently results were confirmed by subjecting RNA samples to Real Time PCR (qPCR) analysis. RNA samples were also screened by DNA microarray hybridization using a MAP specific array.