The objectives of the study are to investigate pharmacy remuneration levels stratified by the number of prescriptions dispensing and the type of nearby medical facilities using the Korean National Health Insurance (NHI) database, and to classify community pharmacies based on the characteristics. Claims data of all community pharmacies were extracted from the Korean NHI database from January 1 to June 30, 2010. A total of 14,985 pharmacies were included for the analysis. The remuneration amounts per pharmacist were directly associated with the number of prescription dispensing, and varied by the type of nearby medical facilities where more than 90% of prescriptions dispensed at the pharmacy are issued from. We classified pharmacies to six groups according to the number of prescription dispensing and the type of nearby medical facilities; (1) pharmacies with equal to or less than 200 prescriptions per month per pharmacist, (2) pharmacies near a general hospital, (3) pharmacies near a regular hospital, (4) pharmacies near a clinic, (5) pharmacies near multi clinics, and (6) pharmacies that do not belong to the above types. Compared to pharmacies near a clinic or multi clinics, pharmacies near a general hospital showed a lower number of prescription dispensing per pharmacist, but the income from dispensing fees was higher (p<0.05). The new taxonomy of community pharmacies can be a useful basis for further policy development in pharmacy remuneration system.