'Mycobacterium avium' subspecies 'paratuberculosis ' ('Map') primarily infects subepithelial macrophages in the ileum of susceptible animals. It has been hypothesized that like other ' Mycobacterium 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 arrest endocytic processing. In this study Differential Display - Reverse Transcription Polymerase Chain Reaction (DD-RT PCR) and Specific Reverse Transcription Polymerase Chain Reaction (RT PCR) were used to assess 'Map' gene expression in 'Map' gD30 during growth in laboratory culture and during growth within BoMAC bovine macrophages. Results from DD-RT PCR were not reproducible and arbitrary primers were unable to amplify differentially expressed mRNA transcripts. However, RT-PCR was successfully applied to identify differentially expressed genes. A housekeeping sigma factor gene, 'sigA, Map' iron regulation homologs, 'furA, furB', and MAP3773, a 'Map' unique gene, 'hspX' and a 'M. tuberculosi's H37Rv protein kinase homolog, 'pknG', were among the ' Map' gD30 genes that were differentially expressed during grown within bovine macrophages.