Clinical practice guidelines (CPGs) are systematically developed statements to assist practitioner and patient decisions about appropriate healthcare for specific clinical circumstances. There is a limited number of studies on guidelines in Turkey. The quality of Ministry of Health guidelines have formerly been assessed whereas there is no information on the other guidelines developed in the country. This study aims to assess the quality of CPGs that are developed by professional societies that work for the health sector in Turkey, and compare the findings with international guidelines. Professional societies that work for the health sector were determined by using the data obtained from the Ministry of Internal Affairs. Inclusion and exclusion criteria were defined for selecting the CPGs. Guidelines containing recommendations about disease management to the doctors, accessible online, developed within the past 5 years, citing references for recommendations, about the diseases over 1% prevalence according to the "Statistical Yearbook of Turkey 2012" were included in the study. The quality of CPGs were assessed with the AGREE II instrument, which is an internationally recognized tool for this purpose. Four independent reviewers, who did not participate in the development of the selected guidelines and were trained in CPG appraisal, used the AGREE instrument for assessment of the selected guidelines. 47 professional societies were defined which provided access to CPGs in their websites; 3 of them were only open to members so these could not be reached. 8 CPGs from 7 societies were selected from a total of 401 CPGs from 44 societies. The mean scores of the domains of the guidelines which were assessed by the AGREE II tool were; 64%, stakeholder involvement: 37.9%, rigour of development: 35.3%, clarity and presentation: 77.9%, applicability: 49.0% and editorial independence: 46.0%. This is the first study in Turkey regarding quality appraisal of guidelines developed by the local professional societies. It adds to the limited amount of information in the literature that comes from Turkey as well as other developing countries.