PurposeThe main focus of this study is to assess the knowledge and practices of healthcare practitioners regarding data sharing, security, and confidentiality, with a focus on the use of health data retrieved from electronic health records (EHRs) for research purposes.MethodsA descriptive, cross-sectional, questionnaire-based survey study was conducted across all academic institutions including all researchers in the medical field in Jordan. Personal and administrative practices in data sharing were assessed through collecting data from respondents.ResultsThe response rate was 22% with an average of 10.25 years of experience in publications. Almost 60% had published at least 1 to 3 studies using EHRs. The prevalence of researchers who “Always” used antivirus software and preserved patient’s information was 75.5% and 92.2%, respectively. However, other personal security and confidentiality measures were not satisfactory. Less than half of health data used in the research was “Always” anonymised or encrypted and only around 44.0% had “Always” used sensitive data with more specificity than normal data.ConclusionConfidentiality and data sharing practices of healthcare practitioners and researchers were generally less than optimal. Efforts from healthcare providers, health institutions, and lawmakers should be put in place to protect the security and confidentiality of electronic patient data.