BACKGROUND: Primary care professionals often manage patients with multiple long-term health conditions, but managing multimorbidity is challenging given time and resource constraints and interactions between conditions. OBJECTIVE: To explore GP and nurse perceptions of multimorbidity and the influence on service organization and clinical decision making. METHODS: A qualitative interview study with primary care professionals in practices in Greater Manchester, U.K. Interviews were conducted with 15 GPs and 10 practice nurses. RESULTS: Primary care professionals identified tensions between delivering care to meet quality targets and fulfilling the patient's agenda, tensions which are exacerbated in multimorbidity. They were aware of the inconvenience suffered by patients through attendance at multiple clinic appointments when care was structured around individual conditions. They reported difficulties managing patients with multimorbidity in limited consultation time, which led to adoption of an 'additive-sequential' decision-making model which dealt with problems in priority order until consultation resources were exhausted, when further management was deferred. Other challenges included the need for patients to co-ordinate their care, the difficulties of self-management support in multimorbidity and problems of making sense of the relationships between physical and mental health. Doctor and nurse accounts included limited consideration of multimorbidity in terms of the interactions between conditions or synergies between management of different conditions. CONCLUSIONS: Primary care professionals identify a number of challenges in care for multimorbidity and adopt a particular model of decision making to deliver care for multiple individual conditions. However, they did not describe specific decision making around managing multimorbidity per se.