Background The use of gut feelings to guide clinical decision making in primary care has been frequently described but is not considered a legitimate reason for cancer referral. Aim To explore the role that gut feeling plays in clinical decision making in primary care. Design and setting Qualitative interview study with 19 GPs in Oxfordshire, UK. Method GPs who had referred patients to a cancer pathway based on a gut feeling as a referral criterion were invited to participate. Interviews were conducted between November 2019 and January 2020, and transcripts were analysed using the one sheet of paper method. Results Gut feeling was seen as an essential part of decision making that facilitated appropriate and timely care. GPs distanced their gut feelings from descriptions that could be seen as unscientific, describing successful use as reliant on experience and clinical knowledge. This was especially true for patients who fell within a ‘grey area’ where clinical guidelines did not match the GP’s assessment of cancer risk, either because the guidance inadequately represented or did not include the patient’s presentation. GPs sought to legitimise their gut feelings by gathering objective clinical evidence, careful examination of referral procedures, and consultation with colleagues. Conclusion GPs described their gut feelings as important to decision making in primary care and a necessary addition to clinical guidance. The steps taken to legitimise their gut feelings matched that expected in good clinical practice.