Tail biting is a common problem in pig production, but genetic studies are impeded by the difficulty of observing it. Even if observations or video recordings are possible, large-scale phenotyping is enormously complex and labour-intensive. Behavioural problems caused by various stressors usually manifest before escalating into damaging behaviour where serious injuries occur. Therefore, it useful to study the precursors of tail biting, which are behaviours termed 'abnormal' such as belly nosing, ear biting and 'tail-in-mouth' to gain insights into the molecular physiology of tail biting. It has been shown that poor sanitary conditions in combination with dietary protein reduction increase the prevalence of tail biting. Since restricting the protein content in the diet is a promising way to reduce nitrogen emissions in pig manure, it is important to investigate whether this measure can lead to a reduction in animal welfare. Even if essential amino acids are substituted, the overall reduction in dietary protein could lead to an increase of abnormal behaviours. Pigs differ in their ability to utilize dietary proteins, which has been shown to be heritable. Therefore, we expect that individuals are not equally affected by protein reduction, because more efficient pigs might better cope with the reduced availability of amino acids required for neurotransmitter synthesis. 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.