Throughout the world, previously extensive areas of natural habitats have been degraded and fragmented, and improving habitat connectivity may help the long-term persistence of species, and their ability to adapt to climate changes. We focused on Borneo, where many remaining areas of tropical forest are highly fragmented, and we assessed the extent to which Protected Areas (PAs) protect highly-connected forest sites. We analysed remotely-sensed land cover data (0.86 km(2) grid cell resolution) using 'Zonation' reserve design software, and we ranked grid cells (rank 0-1) according to forest extent and connectivity. PAs currently cover 9% of Borneo, but <20% of highly-connected cells (i.e. cells with Zonation ranks >= 0.9) lie within PAs. Approximately 65% of highly-connected cells were located above 400 m elevation, although >60% of Borneo's total land area lies below 200 m and only 15% of highly-connected cells occurred in these low elevation areas. These findings were relatively insensitive to assumptions about species' dispersal ability (within the range 1-20 km; representing relatively mobile animal species). The percentage of highly-connected grid cells within PAs could rise from 20 to 50% under proposed new PAs (including the 'Heart of Borneo' project), although many other highly-connected sites will remain unprotected. On-going land-use changes mean that existing PAs in lowland areas are likely to become increasingly isolated within inhospitable agricultural landscapes, and improving connectivity through reforestation and rehabilitation of degraded forest may be required to maintain the conservation value of these PAs in future.