With respect to the release of transgenic woody plants the stability of integrated transgenes and their long-term expression is one of the main objectives in monitoring and risk assessment of genetically engineered plants. A stable integration and expression of the transgenes is particular important for fruit trees, which have an exceptional long production time compared with annual crops. Agrobacterium tumefaciens-mediated transformation of commercially grown apple cultivars was used to increase resistance to the main diseases, like powdery mildew, apple scab and fire blight. Transgenic apple plants were transferred to the greenhouse, grown as own rooted trees or grafted in different scion-rootstock combinations consisting of a transgenic/non-transgenic part. This plant material was used for investigations on stable integration and expression of transgenes. The analyses were carried out using insert-PCR, RT-PCR for gene transcription and ELISA technique for marker protein assay. In 34% of the examined samples neither the transgene nor the neomycinphosphotransferaseII marker gene (nptII) or both genes were anymore detectable. From the remaining samples with a stable integration of the T-DNA, four plant samples did not express the nptII marker gene. Three plants without transcription of the marker gene nptII were tested by a PCR methylation assay. While one sample of the tested plants did not amplify the fragment of the nopalinsynthase promoter (nos promoter), the remaining two plants are assumed to be methylated at the nos promoter site.