Background Waterpipe tobacco smoking prevalence, practice, and the associated health perceptions among dental practitioners have not been previously reported. This study aims to determine the prevalence of waterpipe smoking among dental practitioners and to evaluate their awareness of health hazards of waterpipe smoking, particularly the adverse effects on oral health. Methods This was a cross-sectional questionnaire-based survey among dental practitioners. Surveyed dental practitioners practiced dentistry in the holy city of Al-Madinah Al-Munawarah, a city in the Central-Western Region of Saudi Arabia, and the study was conducted during March 2015. The questionnaire consisted of questions on demographic data, history and practices of tobacco use, and perceptions toward the health hazards of smoking. Dentists were approached at their work places and invited to participate. Descriptive statistics were used to describe the sample's demographic and smoking characteristics, while cross-tabulation and chi-square test were used to determine the statistical significance of association between the groups ( P ≤ 0.05). Results One hundred dental practitioners participated in the survey, with 55 males and 45 females. Twenty-six percent indicated that they were water-pipe smokers. Male gender and cigarette smoking were the only factors to be significantly associated with waterpipe smoking ( P = 0.008 and P = 0.000, respectively). Most participants stated that waterpipe smoking is harmful to health, and the most commonly reported health hazard was respiratory disease, which was reported by 81% of participants. Conclusions Prevalence of waterpipe smoking among dental practitioners is comparable to adult populations but lower than younger populations of university students. Health awareness of dental practitioners regarding waterpipe smoking was judged to be insufficient.