Neisseria gonorrhoeae can be cultured in the saliva of individuals with pharyngeal gonorrhea. The aim of this study was to quantify the gonococcal bacterial DNA loads in the pharynges and saliva among men who have sex with men (MSM) with untreated pharyngeal gonorrhea. Untreated MSM who tested positive for pharyngeal gonorrhea by culture and returned for antibiotic treatment within 14 days at the Melbourne Sexual Health Centre between October 2014 and March 2015 were eligible for this study. The gonococcal bacterial DNA load was measured using real-time quantitative PCR. The median gonococcal bacterial DNA loads in the pharynges and saliva were calculated and compared to culture positivity using the Mann-Whitney U test. A total of 33 men were included in this study. The median gonococcal bacterial DNA load did not differ between the pharynges in men who were culture positive (2.5 × 105 copies/swab) and culture negative (2.9 × 104 copies/swab) (P = 0.166) and the saliva (culture positive, 2.2 × 105 copies/ml; culture negative, 2.7 × 105 copies/ml) (P = 0.499). The bacterial DNA load in the pharynges (P = 0.695) and saliva (P = 0.969) did not differ between who men returned for treatment within 7 days and those who returned 8 to 14 days later. Substantial gonococcal bacterial DNA loads were detected in both saliva and pharynges among MSM with pharyngeal gonorrhea. These findings suggest that gonorrhea can be transmitted via sexual practices involving exposure to saliva, such as oroanal practices (rimming) and saliva use as a lubricant for anal sex.