Clinical pharmacy service is a healthcare service focusing on patients. This concept involves the cooperation between health professionals and has been widely by hospitals abroad Indonesia. While in Indonesia, the implementation of clinical pharmacy is still limited and is not yet optimal. Health professionals perception is very important to develop clinical pharmacy service in the hospital. This study aims to determine perceptions of health professionals on the role of pharmacist in clinical pharmacy services, and the influence of health personnel characteristics on their perception in PKU Muhammadiyah Yogyakarta Hospital. This study is a descriptive non-experimental study. The study was conducted during August 2015 - March 2016. The sampling technique used was total sampling. A total of 96 nurses and 17 doctors were given questionnaire with 11 statements about clinical pharmacy services. Perception of health professionals was analyzed using questionnaire value, while analysis of relationship between the characteristics and respondent’ perceptions used One Way ANNOVA dan Independent Samples T-Test. The results showed that health professionals agreed with the role of the pharmacist in clinical pharmacy service with mean score of nurse group was 0,84 while physician groups 0,8 and total mean score 0,83. The value of the significance from characteristic respondents for age (0,697), sexes (0,158), profession (0,322), length of work (0,08) and interaction with the pharmacist (0,094) does not affect the perception of the respondents. While the value of the significance of the characteristics of the work place (0,002) showed an effect on perception. In conclusion, the physicians that involved to the study and nurses are agreed on the role of pharmacist in clinical pharmacy services. Spearman test showed the characteristics of the age, length of work and interaction with a pharmacist affect the perception towards clinical pharmacy service.