For his commitment to translating medical research into advances in the care of people living with both hepatitis C and HIV, the American Society of Clinical Investigation named Dr. Thomas to its honor list of physician-scientists in 2001. He also was elected into the American Association of Physicians for which he served on Council. He received a MERIT award from the National Institutes of Health. From the Infectious Diseases Society of America, he has received the Citation award as well as the Walter Stamm award for mentoring. He was also recognized by the Johns Hopkins University with the Provost's award for outstanding mentoring.