Among his numerous career honors, Waldmann was the 2007 recipient of the AAI-Dana Foundation Award for Human Immunology (known today as the AAI-Steinman Award for Human Immunology Research) and presented the corresponding award lecture at the 2007 AAI annual meeting. He served as a past AAI representative to the International Union of Immunological Societies Nomenclature Committee and as an associate editor and editorial board member for The Journal of Immunology.

His interest in immunoglobulin metabolism led him, with Warren Strober and R. Michael Blaese, to immunodeficiencies such as hypogammaglobulinemia and protein-losing enteropathies, of which one was named after Tom. Over time, he focused on adult T cell leukemia (ATL), a profound disease that is caused by the human retrovirus, HTLV-I, and which is associated with defective immune function; indeed, with Samuel Broder, Tom showed that ATL cells were a monoclonal population of suppressor T cells.