People in developed countries spend up to 90% of their time indoors. This led to an increased awareness for problems regarding indoor environment in the recent years. It is known that mycotoxins formed by moulds can be harmful to human health.The body burden of mycotoxins is caused primarily by the uptake of cereals and related products but sometimes also by animal products. However the health effects caused by indoor moulds are currently under investigation. Therefore the aim of an investigation program is to study mould-dependent health effects in a burdened population of the city of Leipzig, Germany. To estimate exposure situation house dust samples are collected from loaded apartments. To realise the measurements of selected mycotoxins in house dust the development of a suitable analytical method was necessary. Capillary electrophoresis in combination with a special clean up of the samples was found to be an useful tool for these investigations.