Genome wide association studies (GWAS) determine susceptibility profiles for complex diseases. In this study, GWAS was performed in 26 patients with oligo and rheumatoid factor negative polyarticular juvenile idiopathic artritis (JIA) and their healthy parents by Affymetrix 250K SNP arrays. Biological function and pathway enrichment analysis was done. This is the first GWAS reported for JIA families from the eastern Mediterranean population. Enrichment of Fc gamma R-mediated phagocytosis pathway and response to various stimuli were the leading discoveries, along with the presentation of the strong interaction of JIA-associated genes with HLA cluster in the co-expression network. The co-expression network also presented the direct interaction of a gene in Fc gamma R-mediated phagocytosis pathway, namely GAB2, with BLK, CDH13, IL4R and MICA. The systems biology approach helped us to investigate the interactions between the identified genes and biological pathways and molecular functions, expanding our understanding of JIA pathogenesis at molecular level.