The objective of this study was to conduct the systematic evaluation of methodological quality of clinical practice guidelines (CPGs) in Korea. The authors conducted a very comprehensive literature search to identify potential CPGs for evaluation. CPGs were selected which were consistent with a predetermined criteria. Four reviewers evaluated the quality of the CPGs using the Appraisal of Guidelines, Research and Evaluation (AGREE) Instrument. AGREE item scores and standardized domain scores were calculated. The inter-rater reliability of each domain was evaluated using the intra-class correlation coefficient (ICC). Consequently, 66 CPGs were selected and their quality evaluated. ICCs for CPG appraisal using the AGREE Instrument ranged from 0.626 to 0.877. Except for the "Scope and Purpose" and "Clarity and Presentation domains", 80% of CPGs scored less than 40 in all other domains. This review shows that many Korean research groups and academic societies have made considerable efforts to develop CPGs, and the number of CPGs has increased over time. However, the quality of CPGs in Korea were not good according to the AGREE Instrument evaluation. Therefore, we should make more of an effort to ensure the high quality of CPGs.