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Background: HIV/AIDS still become a serious problem in the world, also in Papua Province-Indonesia. The HIV/AIDS cases in this Eastern province of Indonesia were 15.577 cumulatively in 2013 and 97,2% of cases were heterosexual. Jayapura as the capital city of Papua Province has contributed in high number of AIDS cases, but no much data about condom used among indirect female sexual worker. The aim of this study was to determine the relationship between condom used and vaginal infection among female sexual worker in Jayapura City. Methods: A cross-sectional design was conducted including 141 female sexual workers from bars and massage parlors who were become subjects of this study. A questioner as a tool to identified the condom used and confirmed with microscopic examination from vaginal swab. Chi-square test was used to analyze the data. Results: This study found that 48.9% have permanent partner, 46.1% have experience condom use rejection from partner or client, 72,3% have free condom from the clinic, 76,1% used water based gel as lubricant. 69,5% Indirect female sexual worker had used condom in their last sexual contact. Laboratory analysis from vaginal swab found 24,8% have diplococcus bacteria, 2,1% have Trichomonas vaginalis and 1,4 % Candida albicans. No relationship between condom use and laboratory test results among indirect female sexual worker. Conclusion: More education and information about condom use is needed to raise the awareness, and will support the HIV/AIDS prevention program Keywords: condom, HIV/AIDS, indirect female sexual worker, Papu