Emerging infectious diseases often originate in wildlife, but the complex dynamics of wild animal populations mean that disease control is a major scientific and policy challenge. Culling and vaccination can be effective but the ecological characteristics of wild animals may confound the outcomes of simple management programs. In Britain, badgers Meles meles are a recognized reservoir of Mycobacterium bovis, the causative agent of bovine tuberculosis (bTB), and are involved in its transmission to cattle. Experiments have shown that culling badgers can increase bTB incidence in badgers and cattle, by perturbing the social structure of badger populations, and increasing contact rates. Selectively removal of infected badgers and vaccination of the remainder has recently been advocated as a potential solution. Simulation modelling suggests that this intuitively appealing policy could at best deliver only a minor advantage over thoroughly applying either vaccination or culling, but carries a risk of making the disease problem much worse. We suggest this counterintuitive outcome arises because: 1, not all animals can be caught and tested 2, some genuinely infected animals will be test negative 3, selective culling leaves a larger population of susceptible hosts than non-selective culling 4, some susceptible hosts will not respond to vaccination and 5, perturbation increases contact and transmission rates among a relatively high density population of infectious and susceptible animals.