Clinical pharmacy service is hospital pharmacist service in the ward to maximize the efficacy and minimize the toxicity of a pharmacologic therapy on an individual patient. This service involves the cooperation between pharmacist and other health professionals and has been widely conducted by hospitals abroad. In Indonesia, the implementation of clinical pharmacy service is still limited. Health professionals perception is a very important key to develop clinical pharmacy service in a hospital. This study aims to determine perceptions of health professionals in PKU Muhammadiyah Yogyakarta Hospital on clinical pharmacy services, and the influence of health personnel characteristics on their perception.This study is a descriptive non-experimental study. The study was conducted during August 2015 - March 2016. A total of 96 nurses and 17 physicians were given questionnaire with 11 statements about clinical pharmacy services. Perception of health professionals was analyzed based on questionnaire scores, while relationship ofrespondents’ characteristics with their perceptions was analyzed using One Way ANNOVA andIndependent Sample T-Test. The result showed that health professionals agreed with the role of the pharmacist in clinical pharmacy service with a total mean score of 0.83. The p-value forrelationship between respondents’ characteristic and their perceptions were 0.697for age, 0.158 for gender, 0.322 for profession, 0.08 for length of work, 0.094 for interaction with the pharmacist and 0.002 for nurses’ work place. In conclusion, health professionals in PKU Muhammadiyah Yogyakarta Hospital had a positive perception on clinical pharmacy services and only nurses’ work place influenced the perception towards clinical pharmacy service.