The Javan gibbon is endemic to Java with remaining populations restricted to a few protected areas. This species is currently endangered with habitat loss considered the most serious threat to the long-term viability. Current population estimates (e.g. density, abundance) for the Javan gibbon are limited and variable. As such, there is a critical need to provide thorough monitoring of the existing population. This survey was conducted at five protected areas located in the provinces of West and Central Java from April 2008 to August 2009. The survey areas included Gunung Gede Pangrango National Park, Gunung Simpang Nature Reserve, Gunung Papandayan Protection Forest, Leuweung Sancang Nature Reserve, and Gunung Slamet Protection Forest. The goal of the project was to generate population density estimates for the species that can contribute to the assessment of population trends and conservation priorities in these protected areas. All surveys involved the use of line-transect sampling along transects of 1 to 3.5 km in length with repeated multiple times to generate reliable density estimates. Average group and individual densities were highest at Gunung Gede Pangrango NP (2.5 groups/km2 and 5.7 individuals/km2) and lowest at Leuweung Sancang NR (1.1 groups/km2 and 2.4 individuals/km2). A coordinated approach to the conservation of the existing Javan gibbon population is a high priority and should include long-term population monitoring combined with the assessment of habitat suitability.