The aim of this study was to report a case that underwent a craniotomy after primary pre-operative cerebrovascular and 3D digital subtraction angiography (DSA) showed false results. DSA misdiagnosis and missed diagnosis of aneurysms were found, and the subject was subsequently treated accordingly. This case was analysed to identify: 1) the cause of the false positive and false negative results in DSA, 2) the limitations of 3D DSA and 3) the experience acquired and lessons learned. A 54- year-old spontaneous subarachnoid haemorrhage patient underwent DSA and 3D DSA under local anaesthesia. Results revealed aneurysm at the anterior cerebral A1 end. Considering the excessively large tumour angle circuitry, we decided to adopt craniotomy and clipping under direct vision. Misdiagnosis and missed diagnosis were intra-operatively noticed, and the aneurysm was clipped out. About half a month after the operation, the patient underwent DSA again under full coordination. The results from these two DSAs were compared. An originally suspected aneurysm was merely a pseudo-anterior communicating artery; the real aneurysm was located in the starting zone of A1. Active cooperation (or anaesthesia) made 3D DSA clear and complete. Moreover, the two 3D DSAs were both ineffective in identifying false positive aneurysms because of anatomical variation. 3D DSA is still limited in differentiating or developing anatomical variations of cerebrovascular vessels, thereby causing false positive results. The use of 3D DSA requires full cooperation from the patient. The guiding effect of the clot accumulation area on aneurysms should be considered during operation.