Background Following the increased human immunodeficiency virus (HIV) notification (infection) rates via sexual transmission and increased abuse of new synthetic drugs instead of heroin in China, a study on HIV infections and risk factors among synthetic drugs and heroin users in Beijing was conducted to provide a cue for further development of targets and strategies of HIV/AIDS control and prevention for different drug populations. Methods A total of 428 subjects including 224 heroin users and 204 new synthetic drug users was recruited from communities in Beijing by convenience sampling. chi(2) test was used to compare HIV and syphilis infections between the two subpopulations. Logistic regression models were used to evaluate factors related to HIV, syphilis infections and abuse of synthetic drugs. Results Unbalanced distributions of demographics were detected between the two subpopulations. Compared with heroin users, most users of synthetic drugs were migrants, single and of younger age (age <= 30 years). Ten HIV infections and twenty-four syphilis infections were confirmed among 428 subjects. No significant difference in HIV infection was found between the two subpopulations (crude odds ratio (OR) =0.46, 95% confidence interval (Cl): 0.07-15.80 and adjusted odds ratio (AOR) =1.26, 95% Cl: 0.09-18.28) while four times as many syphilis infections were identified among users of synthetics drugs (AOR=3.92, 95% C/: 1.06-14.56). HIV and syphilis infections appeared to work synergistically. The migrants who were of Han ethnicity, single and who had stayed in Beijing for more than six months were more likely to abuse synthetics drugs. Conclusions The new synthetic drug users and heroin users are different subpopulations. We optimistically speculate that HIV has not yet been introduced into the former in Beijing, but considering higher syphilis infections in synthetic drug users and the role of syphilis in HIV infection, synthetic drug users, as a possible and important driver of the HIV/AIDS epidemic in Beijing, should be paid more attention in HIV prevention and control strategies.