Non-typhoidal Salmonella (NTS) and Campylobacter are common causes of diarrhoea in human immunodeficiency virus (HIV)-positive patients. To investigate if incidence has changed since the introduction of highly active antiretroviral therapy (HAART), we combined data from The Danish Surveillance Registry for Enteric Pathogens and The Danish National Hospital Registry. We found that the incidences of NTS- and Campylobacter-related illness among HIV-positive patients in Denmark have declined since the introduction of HAART, although the incidences remained higher compared to the background population. Moreover our study suggests that there is an increased incidence of Campylobacter-related illness among homosexual men in the HIV-positive population.