We used urinary assays as a non-invasive method to examine corticosterone levels in two outbred strains of male laboratory mice (BKW and CD-1). Measures were taken before and after 2 weeks of pair housing, to examine the effects of social stress. We found that CD-1 mice had significantly higher corticosterone levels compared to BKW mice both before and after pairing. Behavioural measures provided evidence that, when paired, both strains of mice polarised into dominants and subordinates, with a higher overall incidence of aggressive acts in the BKW mice. Some pairings had to be separated to prevent injuries so the pairing procedure introduced a selection for non-aggressive socially tolerant mice. Social status was nevertheless found to be associated with pre-existing differences in urinary corticosterone in the CD-1 strain: mice that later became dominant had overall lower levels of urinary corticosterone compared to subordinates. In conclusion, urinary corticosterone levels indicated clear differences in physiology, likely to be related to the adrenal stress response, dependent on both strain and social status. Thus, this non-invasive measure could help to predict the welfare outcomes of social housing and how these may depend on dominance status, rather than overall levels of aggression, in different strains of mice.