Conscientious objection (conscientious refusal, conscience clause), although usually related with medicine, is gaining increasing importance in pharmacy too. It is a right that gives pharmacists possibility to act according to their own conscience and moral principles which are, very often, in conflict with duties that pharmacists have within their profession. With this paper we explored level of knowledge and support of conscientious objection among pharmacists in community pharmacies in Zagreb area and pharmacy students at the Faculty of Pharmacy and Biochemistry, University of Zagreb. The study was conducted in the period from December 2015 to February 2016, among 209 pharmacists and 423 pharmacy students. To collect data, we used structured questionnaires which questioned sociodemographic characteristics of examinees and also their attitudes, comments and knowledge of the right of pharmacists to conscientious objection. Data analysis was performed using univariate and bivariate statistics. Results showed relatively good knowledge, but also a negative attitude towards conscientious objection, among examinees. Although conscious of pharmacists’ obligation to direct the patient to another colleague or institution, when using conscientious objection, examinees bring up violation of patient’s rights (the right to control over his/her own health and therapy and the right to independent decision-making about medical treatments) as the main downside of conscientious objection. Examinees, especially students, point out that conscientious objection based on religious beliefs doesn’t belong to pharmacies. They think that pharmacist has to be a health professional and don’t let his/her conscience to restrain him/her in performance of his/her duties. Protocols suggested in this study, which would be used when using conscientious objection, could eliminate the danger of menace to patient’s rights, while at the same time protect pharmacists’ rights too. Thereat, of much help would be reconstruction of existing, outdated Codex of pharmacy ethics and deontology and better introduction of ethics in pharmacy to pharmacy students.