Objective To compare the national essential medicines list (EML) and national essential insurance medicine list (EIML) of China with that of the WHO, so as to provide reasonable evidence for the adjustment of new EML and EIML of China. Methods The similarities and differences in the selection, updating, categories, subcategories and the amounts of medicines in the EML and EIML of China and the WHO EML were compared and analyzed. Results There are some differences among the three lists in selecting principles, updating of medicines .The latest version of WHO EML (version in 2007) has 27 categories, including 340 medicines; China EML (version in 2004) has 23 categories and 773 western medicines, containing 23 categories and 225 (66.17%) similar medicines of WHO EML, which accounts for 29.11% of EML of China. China EIML (version in 2005) has 23 categories and 1 031 western medicines, containing 22 categories and 227 (66.76%) of WHO EML, which accounts for 22.02% of EIML of China. China EIML was developed based on China EML. There is little difference in selecting, updating, categories of medicines. Conclusion The difference was obviously found in medicine selection, updating and categories between China EML, EIML and WHO EML. We suggested that our national EML and EIML should be more reasonably selected and updated base on the principals of WHO EML.