Ontology-mediated query answering (OMQA) is a promising approach to data access and integration that has been actively studied in the knowledge representation and database communities for more than a decade. The vast majority of work on OMQA focuses on conjunctive queries, whereas more expressive queries that feature counting or other forms of aggregation remain largely unexplored. In this paper, we introduce a general form of counting query, relate it to previous proposals, and study the complexity of answering such queries in the presence of DL-Lite ontologies. As it follows from existing work that query answering is intractable and often of high complexity, we consider some practically relevant restrictions, for which we establish improved complexity bounds.