BackgroundA population-based study of Chlamydia trachomatis (CT) infections is essential in designing a specific control program; however, no large investigation of CT infections among the general population in mainland China has been conducted since 2000. We aimed to determine the prevalence, risk factors, and associated medical costs of CT among residents, 18–49 years of age, in Shandong, China.MethodsFrom May to August 2016, a multistage probability sampling survey involving 8074 individuals was distributed. Data were collected via face-to-face interviews, followed by self-administered questionnaire surveys. First-void urines were collected and tested for CT and Neisseria gonorrhoeae (NG) using nucleic acid amplification.ResultsThe weighted prevalence of CT infection was 2.3% (95% confidence interval [CI], 1.5–3.2) in females and 2.7% (1.6–3.8) in males. Women, 30–34 years of age, had the highest prevalence of CT infections (3.5%, 2.6–4.4), while the highest prevalence of CT infections in males was in those 18–24 years of age (4.3%, 0.0–8.8). Neisseria gonorrhoeae infection had a prevalence of 0.1% (0.0–0.3) in women and 0.03% (0.0–0.1) in men. Risk factors for CT infections among females included being unmarried, divorced, or widowed (odds ratio [OR], 95% CI 3.57, 1.54–8.24) and having two or more lifetime sex partners (3.72, 1.14–12.16). Among males, first intercourse before 20 years of age (1.83, 1.10–3.02) and having two or more lifetime sex partners (1.85, 1.14–3.02) were associated with CT infections. The estimated lifetime cost of CT infections in patients 18–49 years of age in Shandong was 273 million (range, 172–374 million) China Renminbi in 2016.ConclusionsThis study demonstrated a high burden of CT infections among females < 35 years of age and males < 25 years of age in Shandong. Thus, a CT infection control program should focus on this population, as well as others with identified risk factors.Electronic supplementary materialThe online version of this article (10.1186/s12879-018-3432-y) contains supplementary material, which is available to authorized users.