In 1996, Dr. Halamka joined the faculty of Harvard Medical School, where he integrates his knowledge of medicine and technology, focusing on the use of the Internet to exchange clinical patient data. His research includes security and confidentiality issues, scalability issues, legacy system interfacing, user interface building, and implementation of standards for exchange of administrative and clinical information. As a clinician as well as a researcher, Dr. Halamka uses these tools to improve the care of the patients he treats. He is an active teacher, lecturing on both medical and technology topics to the students, residents, and faculty of Harvard and MIT.

Besides his academic duties at the Medical School, where he also holds the position of assistant professor of medicine, Dr. Halamka serves as the Chief Information Officer of the CareGroup Health System, where he is responsible for all clinical, financial, administrative, and academic information technology serving 3,000 doctors, 12,000 employees, and one million patients. He also serves as chairman of the New England Health Electronic Data Interchange Network and as an associate in medicine in the Division of Emergency Medicine at Beth Israel Deaconess Medical Center.

He has authored three books on technology related issues and founded a software development firm, Ibis Research Labs, Inc. Additionally, he served as a columnist for Infoworld, technical editor of Computer Language magazine, and technology consultant to several startup companies.