This study assessed the effects of intermittent individual housing on behaviour and brain neurotrophins, and whether physical exercise could influence alternate individual-housing-induced effects. Five-week-old BALB/c mice were either housed in enhanced social (E) or standard social (S) housing conditions for 2 weeks. Thereafter they were divided into six groups and for 6 weeks remained in the following experimental conditions: Control groups remained in their respective housing conditions (E-control, S-control); enhanced individual (E-individual) and standard individual (S-individual) groups were exposed every other day to individual cages without running-wheels; enhanced running-wheel (E-wheel) and standard running-wheel (S-wheel) groups were put on alternate days in individual running-wheel cages. Animals were assessed for activity in an automated individual cage system (LABORAS) and brain neurotrophins analysed. Intermittent individual housing increased behavioural activity and reduced nerve growth factor (NGF) and brain-derived neurotrophic factor (BDNF) levels in frontal cortex; while it increased BDNF level in the amygdala and BDNF protein and mRNA in hippocampus. Besides normalizing motor activity and regulating BDNF and NGF levels in hippocampus, amygdala and cerebellum, physical exercise did not attenuate reduction of cortical NGF and BDNF induced by intermittent individual housing. This study demonstrates that alternate individual housing has significant impact on behaviour and brain neurotrophin levels in mice, which can be partially altered by voluntary physical exercise. Our results also suggest that some changes in neurotrophin levels induced by intermittent individual housing are not similar to those caused by continuous individual housing.