Background This study examined substance use and abuse, including nicotine and alcohol, in subjects who were at various stages of a medical career in Dokuz Eylul University Medical School in Turkey. Anxiety and depression levels were also assessed in order to determine the relationship of the substance use and anxiety and depression. Method Using an anonymous, self-administered questionnaire, we surveyed 121 junior, and 52 senior medical students, 73 residents and 80 practicing physicians who completed the questionnaire. Results Alcohol was the most frequently used substance in all groups. Two or more positive responses on the CAGE were obtained for 22.4% of the junior students, 20% of the senior students, 8.9% of the residents and 6.5% of the physicians. Lifetime smoking prevalence was as high as 50%. The age of onset for nicotine and alcohol use was earlier in first-year medical students than the other groups. Benzodiazepines (alprozolam, diazepam) were the most frequently used sedative-hypnotics. The use of illicit substances was rare in all four groups, with cannabis being the most commonly used illicit substance. The junior medical students (23.6 %) had the highest level of anxiety, while the senior students (44 %) had the highest level of depression, assessed by the Hospital Anxiety and Depression Scale. However, the levels of anxiety and depression did not correlate with the levels of cigarette and alcohol consumption. Conclusions Smoking and alcohol abuse amongst medical students and physicians should be taken more seriously because their own attitudes towards substances may influence their professional behavior. There is a need for better education about substances.