Introduction The evolution of medicine during the past few decades has resulted in electronic transformation of patient records which experienced multiple problems such as security, privacy and confidentiality of patient's information. Security, privacy and confidentiality are potentially major problems in electronic health records and no system currently available in the world is 100% secure. The objectives of this study were to describe the major issues related to security, privacy and confidentiality of electronic health information systems and computer based patient record systems and to describe methods currently used to overcome those issues by reviewing published articles. Method These articles were identified by searching the PubMed online electronic bibliographic database [www.ncbi.nih.gov/pubmed] for articles published between January 2000 and January 2013 using the keywords security, privacy, confidentiality, electronic health information systems, and computer based patient record systems. 25 articles were selected for this review after a screening process from among 236 articles identified after the PubMed search. Results All 25 articles (100%) had identified that security, privacy, and confidentiality were major problems with Electronic Health Records. None of them were 100% secure and only two (8%) were Health Insurance Portability and Accountability Act (HIPAA) compliant. Conclusion Safeguarding the security, privacy and confidentiality is a major problem in electronic health records and a major challenge for governments. However, studies on the security, privacy and confidentiality issues were not conclusive. Alternative approaches considering social, cultural and governmental factors may be needed to be taken into account to deal with the security, privacy and confidentiality issues.