Baseline data on health of free-ranging wildlife is essential to evaluate impacts of habitat transformation and wildlife translocation, rehabilitation, and reintroduction programs. Health information on many species, especially great apes, is extremely limited. Between 1996 and 1998, 84 free-ranging orangutans captured for translocation, underwent a complete health evaluation. Analogous data were gathered from 60 semi-captive orangutans in Malaysia. Baseline hematology and serology; vitamin, mineral and pesticide levels; and results of health evaluations, including physical examination, provide a baseline for future monitoring. Free-ranging and semi-captive orangutans shared exposure to 11 of 47 viruses. The semi-captive orangutans had significantly higher prevalence of antibodies to adenovirus (P < 0.0005) and rota (SA 11) virus (P < 0.008). More free-ranging than semi-captive animals had antibodies to Japanese encephalitis virus (P < 0.08) and foamy virus (P = 0.05). Exposure to parainfluenza and langat viruses was detected exclusively in semi-captive animals and exposure to sinbis virus was only found in free-ranging orangutans. There was evidence of exposure to respiratory syncytial virus, coxsackie virus, dengue virus, and zika virus in both groups. Ebstein-Barr virus was ubiquitous in both groups. Prevalence of antibodies against mumps virus changed from 0% in 1996 to 45% in 1998. No antibodies were detected to many important zoonotic viral pathogens, including herpesvirus and hepatitis virus. Prevalence of Balantidium coli and Plasmodium pitheci infections and exposure to mycobacterium was higher in the semi-captive animals. Differences in exposure to pathogens between the groups may be due to environmental factors including differences in exposures to other species, habitat quality, nutritional status, and other potential stressors. Differences in health parameters between captive and free-ranging orangutans need to be considered when planning conservation areas, translocation procedures, and rehabilitation protocols. Because survival of the orangutan is linked to animal and ecosystem health, results of this study will assist wildlife conservation programs by providing baseline health information.