BACKGROUND: Despite the considerable changes in the provision of health care to prisoners in the UK there is little published literature that attempts to examine broader aspects of health and the impact of imprisonment on these, focusing instead on disease specific areas. This is surprising given that one of the main drivers behind the changes was the need for improvements in the quality of care; examining changes in health outcomes should be an important part of monitoring service developments. This study assessed the health-related quality of life of women on entry into prison and examined changes during a period of three months imprisonment. METHODS: This was a prospective longitudinal study involving 505 women prisoners in England. The SF-36 was contained within a questionnaire designed to examine many aspects of imprisoned women's health. Participants completed this questionnaire within 72 hours of entering prison. The researchers followed up all participants who were still imprisoned three months later. RESULTS: The study achieved good response rates: 82% of women agreed to participate initially (n = 505), and 93% of those still imprisoned participating three months later (n = 112). At prison entry, women prisoners have lower mental component summary score (MCS) and physical component summary score (PCS) compared to women within the general population. The mental well-being of those 112 women still imprisoned after three months improved over this period of imprisonment, although remained poorer than that of the general population. The PCS did not improve significantly and remained significantly lower than that of the general population. Multivariate analyses showed that the only independent predictor of change in component score was the score at baseline. CONCLUSIONS: The results highlight the poor health-related quality of life of women prisoners and highlight the scale of the challenge faced by those providing health care to prisoners. They also draw attention to the major health disadvantages of women offenders compared to women in general. While recent reforms may improve health services for prisoners, broader inequalities in the health of women are a more complex challenge.