Objective: The deep-south provinces of Thailand, the border area where the population is majority Malay ethnic, have faced with armed-conflicts for the decade and are a major route for drug trafficking. Several studies have reported concerns about drug problems among local population but the size of drug using population has not been studied. The objective of this study is to estimate the size of drug using population in the deep-south provinces of Thailand. Methods: A cross-sectional survey, including interviews was conducted in 2016. Males aged 18-40 years who had used any drugs in past six months were recruited. Respondent-driven sampling method was used to reach the target population and multiplier method to estimate the size of drug using population. Results: The estimated number of male using drug population in three deep-south provinces was 13,545, making the prevalence of 50.2 per 1,000 male population of this age group, twice as high as the national prevalence. Most drug users were in Pattani (60.6%), followed by Narathiwas and Yala provinces. Kratom is the illicit drug with the highest number of current users (85.2% of all users). The majority of current users (60.6%) used more than one type of illicit drug, with kratom and methamphetamine being the most common combination (25.6%). Conclusion: This study depicts the situation of drug abuse in deep-south Thailand. Kratom was the most popular substance. The high prevalence of drug users in the area should be of concern by stakeholders and interventions to minimize and control the abuse are needed.