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The main purpose of the present study was to investigate the value and effectiveness of functional and morphological magnetic resonance imaging (MRI), in order to assess the extent of brain injury in a hypoxic–ischaemic piglet model, and further to validate that the ischaemic injury was successfully induced. In this way, we also characterized the Harderian gland. MRI was performed at 1.5 T in anaesthetized piglets (n = 10, 12–36 h of age). Magnetic resonance perfusion and diffusion imaging were performed at different time points, before, during and after the induction of hypoxia–ischaemia. The effects following bilateral clamping of the carotid arteries were also assessed by contrast-enhanced magnetic resonance angiography. Morphological assessment included T1- and T2-weighted imaging, and fat-suppressed T1-weighted imaging before and after contrast medium enhancement. Morphological MRI revealed a prominent, well-defined structure located at the eyeball. Magnetic resonance angiography reconstructed with volume rendering showed this structure to be partially enclosed by large venous sinuses. At dissection, when compared with the magnetic resonance images, the deep gland of the third eyelid, the Harderian gland, corresponded to this structure both in topography and in size. By contrast, the lacrimal gland proper presented as a small, soft and pale structure that was difficult to distinguish from the surrounding connective tissue. At histological examination, the Harderian gland consisted mainly of compact areas of tubuloacinar glands with abundant eosinophilic granules. The present MRI demonstration of the Harderian gland was an accidental finding during an investigation to assess the extent of brain injury in a hypoxic–ischaemic piglet model. The combination of MRI and histology made it possible to detect and describe the Harderian gland in pig. It has generally been studied in rodents and lower vertebrates and is reported to possess various endocrine and exocrine functions.