Professor Mallon returned to Ireland in 2007 and has led the development of an active research programme in Infectious Diseases. In 2008 he established the HIV Molecular Research Group, which focuses on translational research into toxicities of antiretroviral therapy, strategies to increase population HIV testing and studies aimed at better understanding immune responses to antiretroviral treatment.
Professor Mallon is a past-president of the Infectious Diseases Society of Ireland, a regional representative for the European AIDS Clinical Society and the incoming Chair of the co-morbidities Guidelines Panel of the European AIDS Clinical Society. Professor Mallon is also the Director of the Wellcome-Health Research Board Irish Clinical Academic Training Programme.