As part of the Third Healthcare Associated Infection (HCAI) Prevalence Survey of the United Kingdom and Ireland, HCAI point prevalence surveys were carried out in Northern Ireland (NI) and the Republic of Ireland (RoI). Here we explore the potential benefits of comparing results from two countries with different healthcare systems, which employed similar methodologies and identical HCAI definitions. Forty-four acute adult hospitals in the RoI and 15 in NI participated with a total of 11 185 patients surveyed (NI 3644 patients and RoI 7541). The overall HCAI prevalence was 5.4 and 4.9 in NI and the RoI, respectively. There was no significant difference in prevalence rates of HCAI, device-related HCAI or HCAI associated with bloodstream infection but there was a difference in meticillin-resistant Staphylococcus aureus-related HCAI (P = 0.02) between the two countries. There were significantly more urinary tract infections and Clostridium difficile infections recorded in NI (P = 0.002 and P < 0.001). HCAIs were more prevalent in patients aged >65 years and in the intensive care unit in both countries. HCAIs were also more prevalent if patients were mechanically ventilated, had had recent non-implant surgery (RoI) or had more recorded HCAI risk factors. This is the first time that HCAI prevalence rates have been directly compared between NI and the RoI. By closely examining similarities and differences between HCAI prevalence rates in both countries it is hoped that this will influence healthcare planning and at the same time reassure the public that HCAI is important and that measures are being taken to combat it.