The increasing efficiency of genetic analyzers together with the decreasing price of DNA sequencing per single nucleotide read, makes the method of individual genomes sequencing more available for diagnostic laboratories. Nowadays genome sequencing applications are predominantly used for research purposes but in nearest future we will be using them in routine patient evaluation as we are using analytic approaches based on Sanger method now. New generation sequencing is a tool which gives the researchers excellent possibilities for the realization of personalized medicine assumptions. However, before we will be able to make full use of it, there are still some questions to be answered, as for example who should perform the analysis, interpret results and finally who should be responsible for data management.