General Practitioners (GPs) and healthcare systems, worldwide, are overwhelmed by the growing number of patients with multimorbidity, particularly in light of the additional complexity and costs involved in treating these patients. While it has been proven that clinical decision support systems (CDSS) play a key role in supporting healthcare decisions, there is little research into their role in the case of multimorbidity. This study examines practice systems currently used in Ireland and evaluates their effectiveness in such circumstances. The findings uncover a number of deficiencies, including: (1) the lack of provision of integrated medical guidelines for multiple chronic diseases within the CDSS, (2) the inability to centralise the patient rather than the disease, (3) the difficulty in seamlessly integrating CDSS into the patient consultation, and (4) the lack of adequate training of GPs on how best to use CDSS in multimorbidity decision making. The study underlines the need for further research into CDSS and multimorbidity, and highlights some of the key issues that must be addressed in order to improve how CDSS support the care of multimorbid patients.