Cheetahs (Acinonyx jubatus) held ex situ can provide an important resource for obtaining new biological information that usually cannot be gleaned from free-living individuals. However, consistent captive propagation of the cheetah, a prerequisite for establishing a self-sustaining population, has not been accomplished so far. This study examined the effect of a husbandry regimen commonly used in ex situ facilities on female cheetahs. Although generally solitary in the wild, zoos frequently house cheetahs in pairs or groups. Using non-invasive hormone monitoring and quantitative behavioural observations, we studied the impact of such enforced social conditions on behaviour and ovarian/adrenal activity. Eight female cheetahs were evaluated for two consecutive 6-month periods, first while maintained in pairs and then as individuals. Subsequently four females were regrouped into two new pairs and monitored for another 6 months. Females in five of six pairings demonstrated prolonged anoestrus and displayed agonistic behaviours. After pair separation all females rapidly resumed oestrous cyclicity. Females in the sixth pair continued cycling throughout the year while consistently displaying affiliative grooming and no agonistic behaviours. Faecal corticoid patterns varied significantly among individuals, but appeared unrelated to behavioural or ovarian hormone patterns. Thus, data appear to indicate that same-sex pair-maintenance of behaviourally incompatible female cheetahs may lead to suppressed ovarian cyclicity. This suppression appears linked to agonistic behaviours but not to any particular adrenal hormone excretion pattern. Results clearly demonstrate the value of applying knowledge about in situ social behaviour to ex situ management practices. Conversely, however, non-invasive hormone monitoring conducted ex situ may help us to identify physiological phenomena of potential relevance for future in situ studies.