This research addressed two important issues concerning conservation of orang-utans in Indonesia, the prevalence of diseases in orang-utans at reintroduction centres and the extent of intra-subspecific genetic variation between isolated populations of Bornean orang-utans. The research was conducted at the Wanariset Orang-utan Reintroduction Centre in East Kalimantan from 1994 to 1997, and at the Biomedical Primate Research Centre in the Netherlands in 1998. Studies were designed to identify and determine the prevalence of diseases, specifically gastro-intestinal parasites, tuberculosis and certain viral diseases. Further studies defined the factors associated with mortalities of orang-utans at the reintroduction centre. A molecular study using mitochondrial DNA was undertaken to determine whether there was significant genetic diversity between six isolated populations of wild orang-utans within Borneo. It was concluded that there are at least four genetically distinct populations of Bornean orang-utans. The findings of this research are discussed in terms of the implications for management policies for reintroduction centres, as well as for the conservation of wild populations.