Background: Upper gastrointestinal endoscopy is the most preferable diagnostic examination for patients over fifty when upper gastrointestinal symptoms appear. However, limited knowledge exists in concerns to the compliance of primary care patients' to the doctors' recommendations for endoscopy.Methods: Patients who visited primary care practices in Greece and experienced upper gastrointestinal symptoms within a 10 days screening study, were referred for an upper endoscopy exam. The patients which refused to complete the endoscopy exam, were interviewed by the use of an open- ended translated and validated questionnaire, the Identification of Dyspepsia in General Population (IDGP) questionnaire. A qualitative thematic analysis grounded on the theory of planned behavior was performed to reveal the reasons for patients' refusal, while socio-demographic predictors were also assessed.Results: Nine hundred and ninety two patients were recorded, 159 of them (16%) were found positive for dyspepsia and gastro-esophageal reflux disease according to the IDGP questionnaire. Out of the above, 131 (83.6%) patients refused further investigation with endoscopy. Patients who refused upper endoscopy were predominantly female (87.8%) (p = 0.036) and over the age of 50. The lack of severe symptoms, fear of pain, concerns of sedation, comorbidity and competing life demands were reported by patients as barriers to performing an endoscopic investigation.Conclusions: Patients with dyspepsia in rural Greece tend to avoid upper gastrointestinal endoscopy, with two major axons considered to be the causes of patients' refusal: their beliefs towards endoscopy and their personal capability to cope with it. Future research examining reasons of low compliance should be carried out in combination with modern behavioral theories so as to investigate into the above.