In response to population declines in several bird species, knowledge of habitat quality provides essential information to optimise conservation and management plans. Traditionally, habitat quality has been estimated by using demographic parameters or direct measures of habitat features, but these approaches are often not appropriate to link population dynamics and habitat characteristics. Alternatively, the study of bird physiological responses to environmental alterations has an extraordinary potential to recognise and quantify the problems or stressors that threaten species and affect individual fitness. The physiological state of birds can be defined from different perspectives. Energetics, biochemistry, immunology and endocrinology each offer a range of valuable tools within the framework of conservation physiology. Here I review some of the most commonly used physiological tools in comparative studies: such as measures of metabolic rate, plasma metabolite profiles, immune status, stress responses and stable isotope analysis. In spite of the obvious limitations in any research project, combining different methods in our studies would be a sound approach to identifying the mechanisms underlying the patterns observed in bird population trends.