Glaucoma is now viewed not just a disease of the eye but also a disease of the brain. The prognosis of glaucoma critically depends on how early the disease can be detected. However, early glaucomatous loss of the laminar functions in the human lateral geniculate nucleus (LGN) and superior colliculus (SC) remains difficult to detect and poorly understood. Using functional MRI, we measured neural signals from different layers of the LGN and SC, as well as from the early visual cortices (V1, V2 and MT), in patients with early-stage glaucoma and normal controls. Compared to normal controls, early glaucoma patients showed more reduction of response to transient achromatic stimuli than to sustained chromatic stimuli in the magnocellular layers of the LGN, as well as in the superficial layer of the SC. Magnocellular responses in the LGN were also significantly correlated with the degree of behavioral deficits to the glaucomatous eye. Finally, early glaucoma patients showed no reduction of fMRI response in the early visual cortex. These findings demonstrate that 'large cells' in the human LGN and SC suffer selective loss of response to transient achromatic stimuli at the early stage of glaucoma. Hum Brain Mapp 37:558-569, 2016.