A 42-year-old man fell acutely ill with decreased consciousness, severe right hemiparesis and total left oculomotor nerve palsy. The non-enhanced CT-scan was without acute pathology. On the CT-angio scan, a thrombus was detected in the basilar artery and in the beginning of the left vertebral artery. Clinically and radiologically the patient had a brainstem infarction due to basilar artery thrombosis, which without treatment is a potentially fatal condition. Intravenous thrombolysis with alteplase was started immediately, which was followed by a thrombectomy. The flow in the basilar artery and its branches was successfully restored. During the following days the neurological deficit completely regressed. Despite clinical evaluation the cause of the ishaemic stroke remained unclarified. Therefore, the patient was diagnosed a cryptogenic stroke.