Objective To compare the newest essential medicine lists (EMLs) of China and the World Health Organization (WHO) in 2009, so as to provide the evidence for the selection, adjustment and implementation of the newest national EML of China. Methods Differences in the procedures of selection, implementation and the categories as well as the number of medicines in 2009 EMLs of the WHO and China were compared by descriptive analysis. Result Principles and procedures of selecting and updating EML of China were based on those of the WHO EML. However, the transparency of procedures, methods of selection, and evidence of efficacy, safety, cost-effectiveness and suitability were not enough. Essential medicines of the WHO were categorized by the Anatomical-Therapeutic-Chemical (ATC) classification system, while those of China were classified by clinical pharmacology. Twenty-one identical categories of the first class were found in the two lists. There were 8 and 3 unique categories in the WHO EML and China EML, respectively. A total of 358 and 255 medicines (including medicines in its explanation) were included in the EMLs of the WHO and China, respectively, with 133 identical medicines as well as 206 and 108 unique medicines. There were 51 antiinfective medicines in China EML, accounting for half of the WHO EML. Forty medicines were the same in both lists, and 11 and 60 anti-infective medicines were unique in EMLs of China and the WHO, except for 40 identical medicines. Among them, 22 and 31 antibacterials were included in the lists of the WHO and China with 17 identical medicines. Antifungal, antituberculosis and antiviral medicines in China EML were fewer than those in the WHO EML. The numbers of the identical medicines acting on the respiratory, digestive, and nervous systems and hormones in the both lists were 1, 7, 9, and 17, respectively, while the unique ones in China EML were 6, 12, 7, and 14, respectively. However, most of them were selected without adequate evidence in efficacy and safety. The medicines acting on cardiovascular system were 19 and 29 in both lists with 14 identical medicines. Some antihypertensive and antiarrhythmic medicines were included in China EML with similar mechanism, whereas some of them were excluded by the EML. Conclusion The total numbers of both EMLs are close to each other with half of the identical medicines. The selection of China EML mostly meets the needs of disease burden in China. However, the transparency of selection and evidence are not enough. We suggest that health authorities should cooperate with other stakeholders to promote the transparency of selection, to enhance the capacity of producing high-quality evidence, to develop related technical documents and guidelines, and to disseminate and monitor the implementation of EML.