We develop a formal framework for comparing different versions of DL-Lite ontologies. Four notions of difference and entailment between ontologies are introduced and their applications in ontology development and maintenance discussed. These notions are obtained by distinguishing between differences that can be observed among concept inclusions, answers to queries over ABoxes, and by taking into account additional context ontologies. We compare these notions, study their meta-properties, and determine the computational complexity of the corresponding reasoning tasks. Moreover, we show that checking difference and entailment can be automated by means of encoding into QBF satisfiability and using off-the-shelf QBF solvers. Finally, we explore the relationship between the notion of forgetting (or uniform interpolation) and our notions of difference between ontologies.