The use of genetically modified (GM) animals in biomedical research has increased during recent years and its ethical aspects have been subject to ongoing academic discussion. In order to reinforce this discussion, we analysed applications submitted to animal ethics committees in Sweden during 2002. The aim was to investigate the researchers' statements concerning the production and use of GM animals, as well as the committees' assessments of the applications. For our analysis, we constructed an analytic form. In part, we included the questions and categories of the mandatory application form, noting for example species, degree of severity regarding pain and distress, the management of pain, and endpoints. In addition, we included our own specific questions and categories, and classified the applications accordingly. In particular we focused on the methods of GM animal production and on the expected clinical symptoms attributable to genetic modification and experimental use. Our analysis, which was partly quantitative and partly qualitative, revealed that applications were often approved by the committees despite containing insufficient information regarding ethically relevant aspects, that the arguments for using GM animals were often unclear, and that some applicants indicated awareness of possible unintentional welfare effects attributable to genetic modification. In more than 36% of the applications, obvious or minor clinical symptoms attibutable to genetic modification were expected. However, we also noted that many applicants emphasised that certain GM animals were to be used without the expectation that the animals would display any clinical symptoms. This was obviously viewed as an ethical advantage.