The social environment of animals can have profound implications on their behaviour and physiology. Naked mole-rats (Heterocephalus glaber) are highly social with complex dominance hierarchies that influence both stress- and reproduction-related hormones. Homeostasis may be affected by aggressive interactions, colony instability and social isolation. Furthermore, naked mole-rat colonies are characterised by a marked reproductive skew; a single female and few males are reproductively active while other colony members are reproductively suppressed. Thus, there are distinct differences in related hormone concentrations between reproductively active and non-active animals; however, this changes when non-reproductive individuals are removed from the colony. We investigated the effects of social isolation and colony disruption on plasma cortisol and progesterone concentrations in non-breeding naked mole-rats. During colony disruption, we found a significant increase in cortisol concentrations in females removed from the colony for social isolation (experimental) as well as in females that remained in the colony (control). Cortisol concentrations were reduced in both groups after experimental animals were paired up. No changes in cortisol concentrations were observed in control or experimental males after removal from the colony or pairing. This suggests that the females, but not the males, found colony disruption and social isolation stressful. Upon removal from the colony, both control and experimental females showed a small increase in progesterone, which returned to basal levels again in the control animals. Experimental females showed a dramatic spike in progesterone when they were paired with males, indicating reproductive activation. The sex difference in the stress responses may be due to the stronger reproductive suppression imposed on females, or the increased likelihood of dispersal for males. It is clear that the social environment reflects on the endocrine correlates of animals living in a colony, and that the colony structure may affect the sensitivity of the animals to changes in their environment.