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Background: The privacy issue in web-based registry systems is very important and patients are concerned about it. Protecting patients' privacy in medical databases is an important challenge in health informatics. Objectives: The aim of this study was to develop an instrument to assess privacy challenges of a web-based liver transplantation registry (WLTR), and to determine the views of patients on the privacy of the implemented WLTR. Methods: This study consisted of two parts: 1) an instrument development phase, in which we developed and implemented an instrument, and 2) a cross-sectional study. The instrument included a total of 59 questions based on literature review. Content validity method was performed to confirm the questionnaire validity and its reliability was evaluated based on the test-retest method. The second phase of the study included all patients who received liver transplantation (n=81) between February 2017 and April 2017 in the only organ transplant center in northeastern and eastern Iran. The data were collected using the instrument that we have developed in the first phase of the study. Data were analyzed by SPSS version 16, using descriptive statistics, Mann-Whitney U test, and Spearman's Rank-Order Correlation test. P-value less than 0.05 was considered statistically significant. Results: In the first phase, a researcher-made questionnaire consisting of 71 questions was prepared based on the extensive literature review. Necessary modifications were made to match the questionnaire with research topic by Delphi technique (12 questions were removed and 10 questions modified). The final questionnaire included 59 questions about demographic information (age, gender, education level), different dimensions of privacy (24 questions), tendency to trust (9 questions), availability of identifiable and unidentifiable health information for different users (18 question), and the goals of using identifiable and unidentifiable health information (8 questions). Reliability was evaluated based on the test-retest method (r=0.82). In the second phase, we determine the views of patients who received liver transplantation on privacy in the WLTR. Most patients (74.1%) stated that they were worried about privacy risks in online systems. The sensitivity to using online personal health information in women was higher in comparison to men (p=0.008). Older people have less tendency to use Internet systems to perform activities (p=0.023). In addition, age had a negative relationship with the convenience of using web-based registry (p=0.033, rho= -239). Regarding the purposes of using the WLTR information from the patients' views, the use of information for purposes of health care had the highest mean, and the use of this information for research purposes had the lowest mean. Conclusions: Designers and developers of these systems must, in accordance with the objectives of the registry program, and the users of these systems, develop policies for protecting the privacy of patients. [ABSTRACT FROM AUTHOR]