Despite the widespread use of inbred mice in research, little is known about aging of the circadian system in female mice, although interactions between female gonadal hormones and circadian rhythms have been established. We investigated the influence of the estrus cycle on circadian aspects of running-wheel activity and changes in the course of aging in female C57BL/6 and C3H/He mice recorded continuously between the ages of 3 and 19 months. In the young, cycling mice the second part of the proestrus night was often, but not consistently, characterized by increased motor activity compared to the remaining estrus cycle nights. After estrus cycling had ceased in the course of ageing, the estrus-dependent day-to-day variability in activity was reduced. The amplitude of the daily rest-activity rhythm decreased progressively after the age of 8 months in C3H/He and 10 months in C57BL/6 mice. The capacity for resynchronisation of activity onset to the LD-cycle was compared in young and old mice after an 8-h phase advance of the LD-cycle. Resynchronisation was significantly slower in old C3H/He mice and unaffected by age in C57BL/6 mice. The circadian period in constant darkness did not change with age in either strain. However, the period was shorter in 17-month old C57BL/6 mice compared to an additional group, which was recorded at the same age, after at least 1-month adaptation to the recording conditions. The results show that the reproductive state as well as ageing influence motor activity patterns of female mice in a strain- and cohort-dependent manner.