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Background Injection drug use is a major public health problem. Oral health problems and the appearance of dental disease among injection drug users (IDUs) are caused by their lifestyle. The aim of the present study was to examine the relations between socioeconomic factors, drug use, and oral hygiene habits on the oral health of heroin drug users. Methods A cross-sectional survey on oral health was carried out as part of UNICEF's research on the biological and behaviours survey among injection drug users in Sarajevo, Banja Luka and Zenica in Bosnia and Herzegovina. A sample of 519 IDUs participated in the survey. Respondent Driven Sampling (RDS) was used to obtain the sample. The data were obtained through face-to-face interviews using a structured questionnaire related to sociodemographic characteristics, duration of drug injection, frequency of drug injection in the last month and oral health. Results Older participants (OR = 1.06; 95% CI = 1.02-1.10), part-time employment (OR = 3.57; 95% CI = 1.02-12.20) and unemployment (OR = 3.23; 95% CI = 1.23-8.33) in comparison to full-time employment as the referent category, and longer duration of drug injection (OR = 1.06; 95% CI = 1.003-1.12) were predictors of bad oral health. A higher level of education (OR = 0.56; 95% CI = 0.39 - 0.79), more frequent tooth brushing (OR = 0.59; 95% CI = 0.49-0.71), and regular dental checkups (OR = 3.30; 95% CI = 1.42-7.67) were predictors of good oral health. Conclusions Socioeconomic characteristics of IDUs as well as their lifestyles may contribute to oral health problems. Heroin drug users have specific dental needs, and programmes to improve their oral health should be an integral part of strategies to prevent addictions including treatments and harm reduction programmes. [ABSTRACT FROM AUTHOR]