Unlike pharyngeal Neisseria gonorrhoeae, less is known about pharyngeal Chlamydia trachomatis in men who have sex with men (MSM). We reviewed cases of pharyngeal chlamydia in MSM from January to December 2019. The overall prevalence of pharyngeal chlamydia was 75/6613 (1.13%; 95% confidence interval (CI) = 0.9-1.14). The median number of sexual partners was three, four (5%) reported throat symptoms and 20 (26%) were HIV positive. Multi-site and concomitant infection was common: rectal chlamydia [39 (52%)], urethral chlamydia [12 (16%)], early syphilis [2 (3%)] and gonorrhoea [14 (19%)]. HIV-positive MSM with pharyngeal chlamydia were older (P = 0.02) and more likely to have had previous syphilis (odds ratio = 4.9; 95% CI = 1.6-14.7; P = 0.005). Further research is needed to explore the characteristics of pharyngeal chlamydia and benefits of increased screening for asymptomatic pharyngeal chlamydia in MSM.