This study has quantified the number of complaints made about doctors to hospitals in Ireland over a five year period. Complaints about doctors represented a minority of overall complaints to hospitals. They predominantly concerned clinical care and communication issues. There were few patient complaints about unprofessional behaviour. Hospitals rarely referred complaints to the Irish Medical Council. Thus current practice differs significantly from that envisaged in the new legislative framework. There is a need to promote transparent, efficient and effective regulation through a standardised inter-agency approach.