National data show that in China mainland unsedated gastrointestinal (GI) endoscopy has been applied in most hospitals for clinical examination, while sedated GI endoscopy is only performed in some hospitals. The purpose of this study was to compare sedated versus unsedated GI endoscopy regarding cost, safety, degree of comfort, tolerance level and overall satisfaction of patients over a 6-month period investigation. From March to September 2011, a questionnaire survey was performed on 1800 patients and 30 physicians at Zhongnan Hospital of Wuhan University and Wuhan General Hospital of Guangzhou Military Command. The patients fell into two groups according to their own decisions: the unsedated group (n=1000) and the sedated group (n=800). After examination, the patients and the physicians were required to fill in a questionnaire form. All the data were analyzed statistically. The results showed that the main factors the patients took for consideration between sedated and unsedated procedures included economy, comfort and safety. The income levels between the sedated and unsedated groups showed significant difference (P<0.01). Most patients in the unsedated group had lower income and were covered by less medical insurance. The tolerance rate was 92.4% vs. 65.5% between the sedated and unsedated group, respectively. 95.5% patients in the sedated group and 72.1% patients in the unsedated group chose the same endoscopy procedure for repeat examination. The survey data from endoscopists suggested the sedated procedure was more comfortable but less safe than the unsedated procedure (P<0.01). In China, unsedated GI endoscopy is now widely accepted by the majority of patients due to low cost and safety. Compared to unsedated GI endoscopy, sedated GI endoscopy is less painful, but more expensive and less safe. With the rapid improvement of people's living standard and the reliability of sedation technology, we expect sedated GI endoscopy will be gradually accepted by more patients.