In April and May 2006, internal conflict in Timor-Leste led to the displacement of approximately 150,000 people, around 15% of the population. The violence was most intense in Dili, the capital, where many residents were displaced into camps in the city or to the districts. Research utilising in-depth qualitative interviews, service statistics and document review was conducted from September 2006 to February 2007 to assess the health sector’s response to reproductive health needs during the crisis. The study revealed an emphasis on antenatal care and a maternity waiting camp for pregnant women, but the relative neglect of other areas of reproductive health. There remains a need for improved coordination, increased dialogue and advocacy around sensitive reproductive health issues as well as greater participation of the health sector in response to gender-based violence. Strengthening neglected areas and including all components of sexual and reproductive health in coordination structures will provide a stronger foundation through which to respond to any future crises in Timor-Leste.