The aim of this study was to gather data on condom use among brothel-based female sex workers in Indonesia and to study the reasons for not using condoms in order to provide new and existing condom promotion programs with information to improve their performance. Quantitative data were gathered by KABP surveys (n = 1450) and a condom diary with a sample of 204 female sex workers. Qualitative data were collected by conducting focus group discussions and in-depth interviews among female sex workers and pimps. Around 53% of sexual intercourses were reported to be protected, and 12% of these protected intercourses were preceded by clients' argumentation against it. Only 5.8% of sex workers consistently used condoms for a 2-week period of observation, and this figure decreased to 1.4% for a 4-week period. Reasons for not using condoms from the clients' side, as mentioned by the sex workers, were perceived less pleasure due to the condom and the belief that clients that are acquainted with the sex workers do not need protection against sexually transmitted diseases (STDs) or AIDS. The main reasons of female sex workers for not using condoms were the beliefs that boyfriends, native Indonesians and healthy-looking clients cannot spread STDs. Another reason stated was that sex workers had already taken other preventive measures, like taking antibiotics. The research also showed that pimps were not very supportive of condom use programs in Indonesia. Condom unacceptability is an important reason for not using condoms for both clients and female sex workers, whereas pimps, who are in the best position to encourage condom use, unfortunately consider condom use as a threat to their business. For the successful introduction of consistent condom use, it is necessary to design interventions for both sex workers and clients and to provide appropriate educational materials and preferred brands of condoms. Also, pimps must be involved in intervention programs.