Our aim is to demonstrate the benefits of using a computer model to support the clinical diagnosis of complex eye motility disorders. For diagnosis and differential diagnosis we compared the clinical data of a patient with suspected monocular elevation deficiency (MED) and the corresponding computer simulation with the simulations of rectus superior palsy, vertical Duane miswiring syndrome and two simulations of asymmetric gaze palsy. We used our biomechanical eye model SEE-KID for the computer simulations, which is partly based on ideas and concepts of the software system Orbit™ by Joel Miller. A young patient with the clinical characteristics of congenital MED, unilateral limitation of up-gaze above midline, with accompanying ptosis on the affected right side, mild head posture, chin-up position, partial binocular functions and Bell’s phenomenon was examined. Pupillary situation, cover test, version and duction movements, saccadic test, Parks–Bielschowsky phenomenon and head tilt test, stereopsis test, Bagolini striated lens test and forced duction test were assessed. Up to the age of 5 years we used the prism cover test in the nine main gaze positions; later we switched to the Hess-Lancaster test for analyzing deviations. We also used our computer model for evaluating the diagnosis and for differential diagnosis of our patient. The simulation results from the SEE-KID model support the diagnosis of supranuclear MED, which can be achieved in the model by varying central innervations, contrary to the modification of muscle forces in the simulation of a rectus superior palsy. It is necessary to distinguish between supranuclear, nuclear, interstitial or peripheral lesions with regard to monocular elevation deficit. Simulations of patients with similar pathologies in a way that the simulations correspond to the patient-measured values support (beside the clinical signs) the diagnosis of supranuclear or infranuclear lesions.