Aim: The purpose of this study was to explore the factors that facilitate and barriers towards the implementation of health education programmes in primary education schools of the prefecture of Achaia, Greece. Methods: The sample of the study included 141 educators from a total population of 218 educators who dealt with the implementation of health education programmes in Achaia prefecture during the school period of 2009-2010. The survey method was used to collect data by means of an anonymous questionnaire. Furthermore, at the beginning of the research process a semi-structured interview was carried out with four teachers to help in the development of the questionnaire items. Two factor analyses were conducted: one for the factors that facilitate and one for the barriers towards the implementation of health education programmes. Results: Findings indicated that the most significant factor that facilitates the implementation of innovative health education programmes is "Knowledge and skills of the Health Education Officer and the teachers", which refers to the scientific knowledge, organizational skills, initiatives and the communicative skills of the Health Education Officer as well as to the teachers' autonomy to select appropriate teaching methods and educational materials. On the other hand, the most important barrier in implementing health education programmes is "Limited experience and attitudes of teachers", which refers to limited teaching experience in health education issues, as well as to professional burnout and the negative attitudes towards these innovative programmes. Conclusions: The Health Education Officer plays an important role in programme coordination by supporting, counselling, giving feedback and providing training/educational materials to teachers. (Contains 3 tables.)