Some notochord cells remain along the axis of the vertebral column after embryogenesis. These 'notochordal remnants' have some similarities, but their biological behaviour varies considerably. They can give rise to benign lesions such as ecchordosis physaliphora (EP) and 'benign notochordal cell tumour' (BNCT), or aggressive ones like chordoma. We review the problems of the differential diagnosis of notochordal remnants apropos of a case of the incidental autopsy finding of EP in a 78-year-old man, who died due to heart infarction. The 6-mm asymptomatic gelatinous lesion was fixed to the basilar artery on its ventral aspect. Small EPs can be easily overlooked in autopsy. Ecchordosis physaliphora and intradural chordoma share some similarities that may be misleading and may even result in the wrong diagnosis and therapy. The recently reported new entity BNCT poses a similar problem. We review the literature illustrating the most important features of notochord-derived lesions and discuss the relationships between these lesions with regard to molecular genetics.