Rare diseases represent a heterogeneous group of approximately 8000 various disorders and affect nearly 8 % of the population. The local and international studies of human genomes help to increase the knowledge about genetic variability of the man and due to effective sharing of clinical and molecular data in the registries enable casual diagnostics of the broad spectrum of rare and complex diseases in 55-65 % of the cases. With the diagnostics in the remaining group of patients, new methods and technologies studying human genome are of importance including genetic and functional analyses of genomic variants and their combinations with the aims to recognize and interpret the significances of the somatic mosaics, genetic heterogeneity of individual disorders, the presence of eventual phenocopy, different penetrance and expressivity of individual mutation and diseases with the oligogenic inheritance. Recently, the increasing significance of analyses of noncoding regions in human DNA were recognized including the impact of repetitive and homologs regions on transcription and structure of mRNA. For the diagnostics of genetic causality in patients is necessary to focus on analyses of biologic fluids, tissues, cultivated cells and animal models prepared by methods of cell reprogramming or directed mutagenesis. In this paper, the overview of methods and their importance and limitation is described including whole exome sequencing (WES), whole genome sequencing, functional and homolog cloning, functional complementation, mapping of genes with the help of binding analyses and matching of the results from individual genome with genetic variability in the adequate population. In our institutions, we performed WES in > 520 patients with successful diagnostics above 50 %. In addition, in our group of 225 patients with rare diseases we compared the result of WES with the results of direct sequencing of individual genes indicated by clinical geneticist from various regions of the country and we recognized much higher diagnostic and economic value of WES. Modern diagnostics of rare diseases is time and money consuming and requires close cooperation between patients, their families, attending physicians, clinical geneticists and experts from various laboratories involved in biologic oriented research. It represents a big challenge for organisers and payers of the health care system. Keywords: are diseases, complex disorders, whole exome sequencing, gene mapping.