BACKGROUND Branchial cleft cysts occur because of a failure of involution of the second branchial cleft. However, as well-differentiated squamous cell carcinoma can mimic branchial cleft cysts, there is a lack of consensus on the appropriate management of cystic neck lumps. OBJECTIVE To report our experience of fine needle aspiration cytology and frozen section examination in the management of cystic neck lumps. METHODS Retrospective case note review of patients managed in the Southern General Hospital, Scotland, UK. RESULTS The sensitivity of fine needle aspiration cytology and frozen section for detecting branchial cleft cysts was 75 per cent and 100 per cent respectively. Two patients who did not undergo intra-operative frozen section examination were either over- or under-treated, which is discussed. CONCLUSIONS Adult patients subjected to surgical excision of a suspected branchial cyst should undergo intra-operative frozen section analysis regardless of clinical suspicion for malignancy. This part of management is critical to ensure patients are offered appropriate treatment.