There are standard procedures for collecting data on numbers of birds at sites being proposed for wind farm development and evaluating collision risk for each key species. However, methods do not work well for all species. Where a local bird population is depleted, empirical data cannot provide estimates of likely collision mortality numbers if that population returns to satisfactory conservation status. Field survey methods are also inadequate for cryptic bird species. Both these problems can be important for evaluation of impacts of proposed wind farms on bird populations protected by the EU Birds Directive. We present an alternative method, based on energy constrained activity budgets and natural history, which permits assessment of likely collision numbers where empirical data are inadequate. Two case studies are presented where this approach has been successfully used to resolve disputed planning applications, one for a hen harrier population where numbers present are much below the population size at designation, and one for a cryptic species (greenshank). Our novel method helps reduce uncertainty in assessments constrained by difficulties in collecting suitable empirical data.