Introduction Down syndrome (DS) is the most common chromosomal disorder. It is accompanied by several comorbidities, which could lead to severe morbidity and mortality. Congenital heart disease (CHD) is one of the most commonly described condition. Objective This study aimed to determine clinical profiles, dysmorphic features, CHD, and DS associated comorbidities in a tertiary center (Cairo, Egypt). Patients and Methods This descriptive study included 290 patients diagnosed with DS, who presented to the Clinical Genetics clinic, Cairo University Children Hospitals, from February 2018 to December 2019. The patients' ages ranged from 2 to 4 years old. All patients were evaluated by full history, clinical examination, anthropometric measurements, and assessment of developmental milestones. Patients' diagnostic investigations including karyotype, thyroid function, and echocardiography were checked. Results The study population consisted of 290 children with DS of which 196 (67.6%) were male, 115 (40%) had CHD, the most prevalent atrial septal defect (ASD), patent ductus arteriosus (PDA), and ventricular septal defect (VSD) accounting for 10.7, 7.1, and 4.2%, respectively. Common dysmorphic features were upward slanting palpebral fissures (98.6%), hypertelorism (97.9%), and sandal gap (60.7%). Thyroid dysfunction was the second prevalent comorbidity, found in 35 patients (12.1%). Global developmental delay was reported affecting language (99%), motor (94.8%), and social (92.8%) domains. Conclusion The prevalence of CHD among children with DS was 40% with ASD, PDA, and VSD being the commonest. Thyroid dysfunction was the second most common comorbidity. The most prevalent dysmorphic features were upward slanting palpebral fissures, hypertelorism, and sandal gap. Developmental delay was very common, language being the most affected domain.