To describe differences in the primary tumour and distribution of cervical lymphadenopathy for cases of nasopharyngeal carcinoma (NPC) and nasopharyngeal non-Hodgkin's lymphoma (NPNHL) using magnetic resonance (MR) imaging. MR images of patients with NPC (n = 272) and NPNHL (n = 118) were independently reviewed by two experienced radiologists. NPC had a higher incidence of tumour invasion associated with the levator and tensor muscles of the velum palatine, the longus colli and medial pterygoid muscles, the base of the pterygoid process, the clivus, the base and greater wing of the sphenoid bone, the petrous apex, the foramen lacerum, the foramen ovale, the hypoglossal canal, and intracranial infiltration. In contrast, NPNHL had a higher incidence of tumour invasion associated with the hypopharynx, the palatine and lingual tonsils, as well as the ethmoid and maxillary sinuses. NPNHL also had a higher incidence of extensive and irregular bilateral lymphadenopathy, and lymphadenopathy in the parotid. NPC more often involved an unsymmetrical tumour with a propensity to invade both widely and deeply into muscle tissue, the fat space, the neural foramen, and the skull base bone. In contrast, NPNHL tended to be a symmetrical and diffuse tumour with a propensity to spread laterally through the fat space and along the mucosa to the tonsils of the oropharynx and hypopharynx. These differences facilitate a differentiation of these diseases using MR images, and enhance our understanding of the biological behavior of these malignant tumours of the nasopharynx.