Background Primary care guidelines for the management of persistent, often 'medically unexplained', physical symptoms encourage GPs to discuss with patients how these symptoms relate to negative emotions. However, many GPs experience difficulties in reaching a shared understanding with patients. Aim To explore how patients with persistent symptoms describe their negative emotions in relation to their physical symptoms in primary care consultations, in order to help GPs recognise the patient's starting points in such discussions. Design and setting A qualitative analysis of 47 audiorecorded extended primary care consultations with 15 patients with persistent physical symptoms. Method The types of relationships patients described between their physical symptoms and their negative emotions were categorised using content analysis. In a secondary analysis, the study explored whether patients made transitions between the types of relations they described through the course of the consultations. Results All patients talked spontaneously about their negative emotions. Three main categories of relations between these emotions and physical symptoms were identified: separated (negation of a link between the two); connected (symptom and emotion are distinct entities that are connected); and inseparable (symptom and emotion are combined within a single entity). Some patients showed a transition between categories of relations during the intervention. Conclusion Patients describe different types of relations between physical symptoms and negative emotions in consultations. Physical symptoms can be attributed to emotions when patients introduce this link themselves, but this link tends to be denied when introduced by the GP. Awareness of the ways patients discuss these relations could help GPs to better understand the patient's view and, in this way, collaboratively move towards constructive explanations and symptom management strategies.