Amphibian declines are occurring on a global scale, and infectious disease has been implicated as a factor in some species. Batrachochytrium dendrobatidis (Bd) has been associated with amphibian declines and/or extinctions in many locations, however, few of the studies have actually performed detailed pathological investigations to link the emergence of the disease with mortality rates large enough to cause the declines. Many studies are based solely on the presence of infection, not disease, because of the reliance on molecular tests for Bd. The emphasis of the importance of Bd combined with easy molecular tests has resulted in poor investigations into amphibian mortality and declines in many areas. The line between infection and disease has been blurred, and a step back to basic pathological and biological investigations is needed as other disease risks to amphibians, such as ranaviruses, are likely being missed. In this article, starting points for proper investigative techniques for amphibian mortalities and declines are identified and areas that need to be improved, especially communication between biologist and veterinarians involved in amphibian disease research, are suggested. It is hoped that this will start a much needed discussion in the area and lead to some consensus building about methodologies used in amphibian disease research.