The aim of this study was to characterise typical Jd lesions in farmed red deer in NZ, by comparing them with well-characterised descriptions of ovine Jd. A secondary objective was to determine whether the histopathology found following experimental infection of both sheep and deer was comparable to that seen in naturally infected animals.Twenty-six orally infected sheep, 5 naturally infected sheep, 8 experimentally infected deer and 8 naturally infected deer were used. Tissue was sampled from the gut mucosae, adjoining mesentery and lymph nodes to track progression of disease from the primary site of infection to the lymph node. Deer and sheep were experimentally infected by oral challenge with Mycobacterium avium subsp. paratuberculosis (Map) isolated from the gut lymphatics of clinically affected deer and sheep, respectively. Independent studies have examined the strain type of Map isolated from naturally infected deer and sheep by IS1311 typing. Using this system deer isolates of Map from deer were 'bovine' strain while sheep isolates typed as 'ovine' Map.There were no differences in histopathology or disease severity seen in either species following natural and experimental challenge. The histopathology seen in deer was comparable to that seen in sheep but some unique characteristics were evident. Deer exhibited foci of caseous necrosis within severe lesions. Macrophages seen in deer lesions often displayed unique ultrastructural features not seen in sheep. These findings highlight the need for increased awareness among pathologists for the unique histopathological characteristics of cervine Johne's disease. The findings show that in red deer (Cervus elaphus) caseated lesions can occur within the intestinal lymph nodes and need to be differentiated from caseated lesions caused by M. bovis infection. While grossly visible caseous lesions occur relatively rarely histopathological evidence of caseation is seen more commonly in deer than sheep.