BACKGROUND: Immune activation due to poor hygienic conditions may affect behaviour, as the immune system and brain are linked through several mechanisms. This putative effect may partly result from increased amino acid (AA) metabolism, affecting brain monoamine levels. As pigs can select a diet that meets their AA requirements, offering them the choice between an AA deficient and AA enriched diet may influence the effects of sanitary conditions on brain neurochemistry and behaviour. METHODS: We investigated the behavioural and neurochemical effects of high (HSC) vs. low (LSC) sanitary conditions on pigs with or without a choice to select between two diets differing in AA concentration in a 2x2 factorial experiment. Female pair-housed piglets (n = 48) were kept under HSC or LSC and were offered either a diet deficient in eight indispensable AA or the choice between the deficient diet and a diet enriched with these AA for 19 days. Behaviour, salivary cortisol, blood tryptophan (Trp) and serotonin (5-HT), and hippocampal/prefrontal concentrations of Trp, related monoamines and their metabolites were analysed. RESULTS: LSC had lower platelet serotonin and plasma Trp than HSC piglets. Hippocampal and prefrontal cortex concentrations of Trp, kynurenine (KYN), kynurenic acid, epinephrine, norepinephrine, 5-HT, dopamine (DA), 5-hydroxyindoleacetic acid and homovanillic acid (HVA) were lower for LSC than HSC piglets. LSC piglets had lower KYN/Trp ratios in the hippocampus and, if without dietary choice, in the prefrontal cortex. LSC piglets showed less play behaviours. Piglets without a dietary choice had lower plasma Trp, higher hippocampal HVA/DA turnover, and spent more time on damaging behaviours. No effects on salivary cortisol were found. CONCLUSIONS: A decline in health status induced by poor hygienic conditions reduced platelet 5-HT, blood and brain Trp, as well as brain neurotransmitter concentrations, and negatively influenced behaviour of pigs. There was no impact of offering a choice of an AA-enriched or AA-deficient diet on these effects of sanitary conditions, possibly due to low intake of the AA-enriched diet.