We present an approach for querying collections of heterogeneous linguistic corpora that are annotated on multiple layers using arbitrary XML-based markup languages. An OWL ontology provides a homogenising view on the conceptually different markup languages so that a common querying framework can be established using the method of ontology-based query expansion. In addition, we present a highly flexible web-based graphical interface that can be used to query corpora with regard to several different linguistic properties such as, for example, syntactic tree fragments. This interface can also be used for ontology-based querying of multiple corpora simultaneously.