Gene copy number variation (CNV) has been found to be common in the human genome, however, in plants, it has not been as widely studied. CNV analysis in Pinus sylvestris has been undertaken using real-time PCR in our laboratory. Genes analysed include the thaumatin-like protein (TLP) gene, defensin 2, and Pinus sylvestris pinosylvin synthase gene, as well as some genes involved in the lignin biosynthesis pathway. Elevated copy number of the TLP gene was demonstrated to coincide with higher increase of TLP gene expression in inoculated samples compared to samples with lower TLP gene copy number. CNV analysis of material in the pine breeding program will reveal the extent of this variation and enable determination of correlation with resistance. One of the main problems for real-time PCR CNV analysis in Scots pine is the selection of reference individuals with defined gene copy numbers. However, further investigations will allow for the identification of individual trees with pre-determined gene copy numbers, and the use of multiple control genes will increase the confidence of detected CNV polymorphism. In this poster we compare two strategies of molecular genetics assisted selection towards H. annosum resistant Scots pines – use of gene copy number variation compared to use of gene expression analyses.