Tail biting is a common problem in pig production, but genetic studies are impeded by the difficulty of observing it. It is a broader phenomenon that begins before lesions manifest. Therefore, precursors of tail biting, such as oral and nasal manipulation of conspecifics, should be studied. However, the molecular physiology underlying those behaviours is not well understood. Here we show that gene expression profiles in the hypothalamus of 73 non-tail-docked pigs fed a protein-reduced diet differed between individuals showing abnormal and normal behaviours. We found that differences in the expression of genes involved in neurotransmission, notably in dopamine, serotonin and GABA, and G-protein coupled signalling, energy metabolism and appetite. Our results demonstrate that abnormal behaviours have distinct signatures in the brain, which could be partly caused by genomic variation. These insights can lead to a better understanding of the biological mechanisms involved and thus may ultimately inform genomic selection programmes.