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Aim The aim of this study was to determine the early ophthalmic and electrophysiological features of Joubert syndrome (JS) in young Egyptian children and compare them with other studies. Patients and methods A prospective study was conducted of 10 children who initially presented with neurologic deficits and diagnosed clinically, with radiologic confirmation and secondary molecular diagnostic testing. A comprehensive paediatric, neurologic and ophthalmic evaluation was performed, including visual electrophysiology and ocular examination in conjunction with confirmed determination of probable and known causative variants in Joubert-associated genes. Structural and functional deficits were observed among the individuals within the cohort and compared with reported frequencies of these defects in prior reports. Results Patients’ ages ranged from 14 months to 4 years. Known causative mutations were found in eight of them and five (genes) with confirmation of separate alleles by parental testing. In two cases, molecular confirmation of the diagnosis was not obtained. The spectrum of observed abnormalities includes epicanthic folds, hypertelorism, ptosis, nystagmus, strabismus, lid retraction and chorioretinal degeneration. There were also delayed flash visual evoked potential (VEP) in all 10 cases. The electroretinogram responses (both scotopic and photopic responses) were greatly varied from normal to severely reduced responses, which have been previously reported. These abnormalities allow for subcategorization of the JS, which may correlate with the observed mutations. Conclusion Association of these findings with an expanded clinical definition of Joubert is warranted. The clinical subtypes of JS may be associated with specific types of mutations in the causative genes. This report, which evaluates the findings in a relatively young cohort, provides a unique opportunity to consider the earliest manifestations of JS that may lead to early recognition and appropriate genetic testing to confirm the diagnosis. Clinical findings beyond those identified in this report and by prior publications should be evaluated as potentially independent of the primary genetic condition rather than assuming that each new finding is part of the same syndrome.