BACKGROUND: Neisseria gonorrhoeae infection remains prevalent, and the emergence of antimicrobial resistance has made the treatment and control of gonorrhea more difficult. Therefore, it is important to compare isolation methods and transport media to overcome gonorrhea via epidemiologic understanding and to determine co-infection rates with other sexually transmitted diseases among primary-care hospitals. In this study, we determine the recovery rate of transferred specimens according to type of transport media and co-infection rate using PCR. METHODS: Genital specimens were collected at three primary-care hospitals from January 2010 to November 2012 using transgrow media and commercial BD transport media. Culture and multiplex PCR were conducted to isolate N. gonorrhoeae. RESULTS: Among 162 specimens, 57 (35.2%) isolates were recovered, and 146 (90.1%) specimens were positive for multiplex PCR. The recovery rate was 29.9% (78/261) using transgrow media and 19.2% (50/261) using BD transport media. The most common co-infected bacteria with N. gonorrhoeae was Chlamydia trachomatis (15.8%), followed by Mycoplasma hominis (6.2%) and M. genitalium (3.4%). CONCLUSION: Under general transport conditions, the rate of recovery of N. gonorrhoeae was as low as 19.2-29.9% depending on the type of transport media, suggesting that molecular diagnostic methods are required to detect the remaining 70% of gonorrhea-infected patients. Co-infection with other sexually transmitted diseases was not rare, and other tests for accurate additional antimicrobial regimens should also be considered.