The purpose of the study was to describe the occurrence of the most common complaints related to MSDs in Czech dentists and to assess the risk factors affecting them. A questionnaire survey of 581 Czech dentists (the response rate 72.6%) was conducted in 2011. The questionnaire ascertained general information about the respondents, their work habits and environment along with the occurrence of musculoskeletal disorders. The respondents filled out the questionnaires during the educational events organized by the Czech Dental Chamber. At least mild difficulties associated with the motoric system were reported by 96.9% of the respondents, with 66.3% of respondents reporting moderate or major difficulties. Back and neck pain followed by shoulder pain and headache were the most common complaints in our sample. According to our data: age, gender, length of practice, a history of serious MSDs, the occurrence of MSDs in blood relatives, the perception of work as psychologically demanding, and especially a perceived moderate/bad general health were significantly associated with the four most common musculoskeletal complaints. Some of the factors were found as protective. This study suggests that MSDs represent a significant burden for Czech dentists and further research is needed to elucidate this issue.