This paper discusses the development of a methodological approach to classify hospital pharmacies according to their performance, measured by structure and process indicators. The method considers the influence exerted on performance by the level of care in the hospital and the interdependence among pharmaceutical activities. Algorithms for assessing performance of hospital pharmacies were constructed for each level of care. Different weights were used for core activities in the pharmacy and other specific activities, according to the level of care in the hospital where the respective service was provided. This methodology allowed classifying hospital pharmacies from best to worst, based on performance. Independently of level of care in the hospital, no hospital pharmacies were classified as high-performance, and more than 50% were classified as low-performance.