The importance of pathogens and parasites in the dynamics of natural populations is becoming increasingly recognized. The study of the ecology of wildlife diseases has emerged as a mature discipline with rapid advances in both the formulation of theory and application of these models to real-world wildlife populations (e.g. Anderson & May 1982; Grenfell & Dobson 1995; Hudson et al. 2002; Delahay et al. 2009). The modern synthesis of wildlife disease ecology thus presents an extremely good example of the progress that can be made when theoreticians and empiricists work hand-in-hand to challenge models with data. In parallel with these academic developments has been the wider recognition that not only do zoonotic diseases present very significant challenges to public health and human livelihoods but disease also plays an important role in biodiversity conservation (Daszak et al. 2000). Whilst the main causes of declining biodiversity are habitat loss and fragmentation, hunting and harvesting, and the spread of invasive species, disease is an increasing risk for the animals left in the remaining habitat patches as they come into contact with expanding human populations and their domestic animals (Macdonald & Laurenson 2006). There are now multiple examples of pathogens being implicated in the decline or extinction of species as diverse as frogs, turtles, birds and carnivores in a range of ecosystems around the world (Hudson et al. 2002). In common with other areas of conservation biology, the management of wildlife disease requires an evidence-based approach. As the leading international journal publishing ecological science with management relevance, the Journal of Applied Ecology can play a key role by bringing the best research on wildlife diseases to a global audience of applied ecologists and conservation practitioners. This research can have real-world impact beyond the usual metrics of journal impact factors and university research assessment exercises. This can be illustrated with two examples drawn from recent papers published in the journal. The incidence of bovine tuberculosis (BTB) has risen in UK cattle herds and the failure to control the disease has been linked to the persistence of a reservoir of infection in co-existing European badgers Meles meles. The culling of badgers has formed a component of BTB control policy since the 1970s, despite variable effectiveness. A large-scale trial was conducted in the UK during 1998–2004 to evaluate culling as a strategy to control BTB in cattle. This research demonstrated that whilst BTB was locally clustered in both badgers and cattle, localized culls of badgers did not reduce the incidence of BTB in cattle (Donnelly et al. 2003; Woodroffe et al. 2005). Culling badgers had a profound impact on their spatial organization and this in turn could lead to the spread of BTB infection (Woodroffe et al. 2006; Jenkins et al. 2007). The overall, somewhat awkward, conclusion was that badger culls had both positive and negative impacts on the control of the disease (Donnelly et al. 2006; Hone & Donnelly 2008). This research has reached a very wide audience and, at the time of writing, the UK Government's policy is not to issue licences to cull badgers for BTB control, despite considerable controversy amongst stakeholders. In addition to being a major public health burden in much of the developing world (Knobel et al. 2005), rabies presents a significant threat to population viability of several species of endangered wild carnivores (Laurenson et al. 1998). Recent work in Tanzania and Ethiopia has gone a considerable way to identifying the reservoirs of infection of rabies and developing practical control measures. Long-term studies in the Serengeti suggest that the reservoir for rabies is a multi-host community where domestic dogs Canis familiaris are the only population necessary for persistence but wild carnivores contribute as non-maintenance populations (Lembo et al. 2008). Control strategies that target domestic dogs should therefore have the greatest impact on reducing risk of infection to humans, livestock and wildlife (Cleaveland et al. 2007). In Ethiopia, rabies threatens the persistence of the Ethiopian wolf Canis simensis, an endangered canid restricted to a few isolated Afro-alpine ranges in the Ethiopian highlands. Several lines of evidence indicate that the reservoir for rabies in this ecosystem is the increasing population of domestic dogs and control strategies have focussed on domestic dog vaccination (Haydon et al. 2002; Randall et al. 2006). An outbreak of rabies in 2003 was controlled through the targeted vaccination of wolves to contain the spread of rabies through habitat corridors between subpopulations, and required only low vaccination coverage (Haydon et al. 2006; Knobel et al. 2008). Together, these long-term studies have established a new paradigm for disease management for endangered species and will be an important model for other conservation projects. With this history of publishing some of the most influential recent papers on the management of wildlife disease, the Journal of Applied Ecology is delighted to pull together a new selection of disease management papers in this Special Profile. In the first paper, Cross et al. (2009) describe a long-term study assessing the effects of BTB on the African buffalo Syncerus caffer population of Kruger National Park in South Africa. BTB prevalence varied spatially and increased over the period of study but the disease appeared to have relatively little impact on buffalo breeding success, risk of predation by lions Panthera leo, or population growth rates. Overall, the demographic impacts of BTB were undetectable despite the availability of detailed long-term population data. The study highlights the challenges of determining the impacts of chronic diseases on wildlife populations, particularly for long-lived species where the effects may occur over time-scales that coincide with natural succession and anthropogenic change. In the second paper, Kilpatrick et al. (2009) use a model integrating both ecological, population and epidemiological data to assess the spatio-temporal risk of transmission of brucellosis from bison Bison bison to cattle around the Yellowstone National Park in the USA. The maintenance of brucellosis-free status in livestock provides significant economic benefit to the cattle industry; thus, the presence of the disease in the Yellowstone bison is the source of considerable controversy. The model demonstrates that the risk of transmission of brucellosis from bison to cattle outside the park is highly variable in space, time and frequency, and can be predicted by climatic conditions and the abundance of bison. This variability offers potential for focussed adaptive management that can reduce the financial costs of brucellosis management, reduce the need for culling bison, and maintain very low risk for the cattle industry. Adaptive disease management is also the focus of the third paper in this Special Profile. Wasserberg et al. (2009) develop a multi-state computer simulation model as a tool for adaptive learning and managing chronic wasting disease (CWD) in white-tailed deer Odocoiles virginianus in Wisconsin, USA. CWD is an emerging neurodegenerative prion disease belonging to the family of transmissible spongiform encehphalopathies (TSE) and is the only infectious TSE in free-living animals. The potential detrimental effects of CWD on deer populations together with human health concerns have led management agencies to seek effective control strategies which involve either selective or non-selective culling. The results of the model showed that CWD has spread slowly within Wisconsin and epidemics are expected to last for decades. CWD prevalence is lower in hunted than in non-hunted populations, but at a higher prevalence, the disease competes with hunting to reduce deer abundance. This study demonstrates the value of an adaptive management approach with a predictive modelling framework to evaluate alternative epidemiological control strategies. Finally, two methodological papers (Frantz et al. 2009 and Conn & Cooch 2009) demonstrate the importance of applied disease management problems in contributing to the development of cutting-edge analytical tools in ecology more generally. Conn & Cooch (2009) develop a very broadly applicable method for estimating state transition probabilities from mark–recapture data – a key issue because an individual's state (e.g. age, sex, reproductive maturity) is often a fundamental determinant of their vital rates (survival, fecundity). However, sometimes field data cannot unambiguously assign an individual to a particular state. Rather than the current practice of removing any datapoints for which state is uncertain from their analyses, Conn & Cooch use a case study of the disease status of house finches Carpodacus mexicanus to demonstrate a method for using these ambiguous data in a model of survival and capture probability as a function of disease state. Their approach produces parameter estimates that are substantially more precise than those obtained using previous methods. In the final paper in this Special Profile, Frantz et al. (2009) also uses an example from disease ecology to tackle a fundamental question in ecology more generally – how to separate genetic data into clusters in order to estimate spatial population structure. This is particularly pertinent for disease ecology as disease spread is fundamentally related to spatial structuring of populations. Their study question concerns the likely spread of Classical Swine Fever in a wild boar Sus scrofa population – an issue of major applied significance due to the disease's severe economic effects. Their study strikes a note of caution, that the relatively new Bayesian clustering methods have the potential to produce biased results which could feed through into erroneous designation of conservation or management units. The main aim of the Journal of Applied Ecology is to increase the profile of research that combines the highest standards of ecological science with direct relevance to environmental management and conservation. The papers presented in this Special Profile, and the disease management papers which have been published in the journal in recent years, suggest that the connection between good science and real-world problem-solving is particularly well developed in the study of wildlife diseases. The editors look forward to receiving many more contributions in this area in the future.