Background: The ratio of anxiolytics to antidepressants is an indicator of the quality of treatment of depression and anxiety in primary care. The objective of the study was to investigate the prescription of anxiolytics and antidepressants among Slovenian family physicians, including patient demographics and possible time-trends. Subjects and methods: An exploratory survey and register-based analysis of anxiolytic and antidepressant prescriptions in 2005 and 2008 was performed. Drugs included in the study were classified according to an Anatomical-Therapeutic-Chemical (ATC) drug classification system, and ATC data were used to calculate defined daily doses (DDD) per 1,000 practice population per day. Descriptive analysis of anxiolytic/antidepressant ratio by patients’ age, gender and region of residency was performed. Results: Total amount of prescribed antidepressant drugs increased by 45% during the observed 3-year period, while total prescribing of anxiolytics decreased by 14%, leading to the anxiolytics/antidepressants ratio diminishing from 1 to about 0.5. The highest reduction in the ratio was observed in the northeast region, characterised by high social deprivation and one of the highest suicide rates in Europe. The highest prescribing of anxiolytics and antidepressants was observed in the central region around the capital Ljubljana. Conclusions: The reduction of anxiolytic prescribing and increase in antidepressant prescribing indicates improvement in prescribing practice of Slovenian family physicians. There are big variations in prescribing among different Slovenian regions, which are attributable to the number of psychiatrists and access to psychiatric treatment.