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Monitoring the health of wildlife populations is important for understanding and controlling the risk of infections to livestock, humans and/or other wildlife. In this paper, we analyse the results of surveys of parasites and non-specific signs of diseases carried out on organs from 638 red and 107 sika deer culled in four regions of Scotland between 1991 and 1997. Infections of the lung by Elaphostrongylus spp. were significantly greater in red than sika deer. Older animals were more heavily infected with Elaphostrongylus spp. and Sarcocystis spp., and infections with Sarcocystis spp. tended to be heavier in more recent years. The results suggest that a combination of key indicator parasite species and non-specific signs of disease may be useful for monitoring the health of wildlife populations at a national scale. However, they also demonstrate that such monitoring needs to be long-term, carried out according to standard protocols and at an appropriate resolution to enable integration with data on other potentially influential environmental factors.