Multifactorial diseases and traits have complex etiology and there is evidence that both environmental and genetic factors contribute to the disease. In the beginning most of the research of multifactorial traits was based on studies of single hypothetical candidate genes. However, lately the availability of relatively inexpensive microarrays allowing the analysis of thousands of single nucleotide polymorphisms (SNPs) in one experiment has made it possible to identify genetic variation in non-hypothesis driven manner. Also as regions in human genome are not inherited completely independently but rather in haplotype boxes there is a possibility to impute the missing data on the basis of human whole genome reference genomes so that association analysis can be performed on the set of complete genomic SNPs. The use of such whole genome association studies (GWAS) has resulted in the identification of genes involved in the etiology of autoimmune disorders. The aim of our project is to define new candidate genes for multifactorial diseases, with main focus on rheumatoid arthritis (RA) using GWAs approach but also to apply same approach for the study of differential response of patients with RA to therapy with different biological agents (anti-TNF, CD20 antibodies) as well as to study of genetic determinants of chronic pain in RA patients and other populations.