Background The eye is second only to the brain as an individual organ in its frequency of involvement in genetic disorders. The array of ocular findings associated with developmental disorders, metabolic diseases, and chromosomal anomalies is endless. Aim To determine the prevalence and describe types of ocular malformations among patients with genetic disorders attending the Genetic Clinic of Alexandria University Children’s Hospital from January 2015 to December 2017. Patients and methods In this study, 354 patients were included. Patients’ data were collected from records as follows: the age and sex of the patients, residence, parental consanguinity, family history, pre/perinatal history, and data of general examination and ophthalmic examination. Results Of 354 patients who were enrolled in this study, 83 (23.4%) patients had genetic ocular malformations, 16 cases had corneal clouding, 15 cases of ptosis, 10 cases of strabismus, nine cases of refractive errors, and six cases of microphthalmia. The age variation in the study was between 8 days and 14 years, and 55.4% of cases were below the age of 2 years. Male : female ratio was 1.1 : 1. Overall, 61.4% of cases had positive history of consanguineous marriage, and 9% of cases had a positive prenatal history. Moreover, 4.8% of cases with ocular malformations had chromosomal abnormality, in which 3.6% were numerical (Trisomy 13) and 1.2% were structural (deletion 18q). Genetic diseases associated with ocular malformations could be classified into isolated (nonsyndromic) disorders, which represented 3.6%, and syndromic disorders, which represented the remaining 96.4% of cases. Isolated disorders included primary microcephaly (2.4%) and blepharophimosis, ptosis, and epicanthus disease (1.2%), whereas the syndromic cases included chromosomal disorders (4.8%), metabolic disorders (26.5%), syndromes with primary dermatological abnormalities (7.2%), syndromes with primary skeletal abnormalities (19.2%), syndromes with endocrine/growth retardation (28.6%), syndromes with primary neurologic abnormalities (7.2%), and others (4.2%). Conclusion Overall, 23.4% of patients with genetic syndromes had ocular malformations. The most common anomaly was congenital corneal clouding (19.3%) followed by ptosis (18%), strabismus (12%), refractive errors (10.8%), and microphthalmia (7.2%) in the order of frequency.