Background Palacky University Faculty of Medicine Centre for clinical practice guidelines is the independent academic centre focused on guidelines methodology.

Objectives The aim of this study is to analyse methods of development, adaptation, implementation and evaluation of CPGs in the Czech and Slovak Republic from 2010 to 2013.

Methods The database of all Czech and Slovak CPGs and specialty societies was developed in 2010 and updated on a regular basis. The analysis of methods of development was made. AGREE II instrument was used both in Czech and English version to evaluate quality of some CPGs.

Results There are 112 Czech specialty societies and the national Reference Centre developing CPGs. 1331 CPGS were developed till 2013 in total with increase of 33% between 2010 and 2013. The number of adopted international CPGs has increased significantly. Majority of CPGs have not stated funding and conflicts of interest. In the Slovak Republic, there are 125 specialty societies and the Ministry of Health developing CPGs. 342 CPGs were developed till 2013. Majority of CPGs were developed by government. A few CPGs stated non-governmental funding, which is always a private company support.

Discussion There has been increasing number of developed CPGs in both countries. Standardised high quality methods are not used systematically. High quality methodology was developed and used by Czech National Reference Centre.

Implications for Guideline Developers/Users There should be high quality methods used for CPG development. The developing bodies should adopt methodology already exist in the Czech Republic.