We investigated bed site preference of the Bornean orangutans (Pongo pygmaeus) in the primary (PF) and secondary (SF) forest, East Kalimantan Indonesia. We observed trees with beds along 15.85 km line transects (21 transects) and surveyed available trees for beds on 4 plots (0.2 ha/plot) for each forest. We observed 860 beds on 115 species of trees (N= 423 beds in PF; 437 beds in SF). In PF, orangutans used 57 different tree species for their beds from the 72 tree species available to them and in SF, they used 72 tree species from the 92 tree species. Orangutans preferred 2 families of trees in PF and also in SF. Percentages of bed sites which the preferred tree families occupied and the percentages of tree occurrence in the forest composition were as follow: in PF 57.6% (244/423) and 11.64% for Lauraceae; 5.44% (23/423) and 1.61% for Ebenaceae; In SF 35.7% (156/437) and 11.34% for Lauraceae; 25.63% (112/437) and 7.66% for Myrtaceae. Analyses of trees size showed that orangutans preferred relatively larger trees with DBH > 41 cm in PF and SF they preferred smaller trees (21 < DBH < 60 cm). There were variations in bed sites preference between the primary and the secondary forests as the consequences of the different forest structure.