Vaughan is the recipient of several awards and is the lead investigator of a national schizophrenia research bio-bank and lead investigator on a population-based longitudinal study of children. He has over 220 publications in the areas of schizophrenia and other psychotic disorders, depression, post-traumatic stress, mental health care delivery in general practice, child psychiatry, cognitive neuroscience, genetics, mental health service evaluation, epidemiology, alcohol and drug abuse, psychotherapy and health economics.