Feather pecking is a major welfare problem in egg production. It may be caused by genetic, physiological and environmental factors. The main aim of this study was to uncover gene expression variability in brain tissue between individuals from high feather pecking and low feather pecking groups using the Chicken Gene Expression Microarray. In total, 313 signals were initially identified as significant (P ≤ 0.05) for the fold change higher than two. A subset of functional candidate genes including downregulated (GLUL, TSPO, MAOA) and upregulated (HTR1B, SIP1, PSEN1) transcripts was subjected to quantitative PCR validation. The significance level and direction of the fold change in gene expression observed by the microarray analysis were confirmed for four genes (HTR1B, SIP1, PSEN1 and GLUL). Newly identified candidate genes play an important role in neurotransmission and psychopathological disorders and can be considered as potential genetic components involved in complex feather pecking behavior. It can be concluded that this study has revealed some interesting differences in gene expression between high and low feather pecking groups and helped to approach elucidation of the genetic foundations of feather pecking.