This comparative cross-sectional study was conducted in the pediatric daycare unit, Hospital Universiti Sains Malaysia to determine the prevalence of craniofacial deformities (CFD) and the association between these deformities and different clinical presentations among thalassemia patients. Patients were classified as either craniofacial deformity positive (CFD+) or craniofacial deformity negative (CFD-) by two examiners based on the presence or absence of deformity of the cheeks, frontal and/or maxillary bones. Fifteen clinical parameters were compared between the groups. Nineteen out of 43 patients (44.2%; confidence interval, 30.2-58.2%) had craniofacial deformities (CFD+). Both groups were comparable among the clinical parameters studied. Patients in the CFD+ group did not start their blood transfusions significantly earlier than the CFD- group (p = 0.50) and had a nonsignificantly lower mean pretransfusion hemoglobin level than the CFD- group (p = 0.71). Patients receiving regular monthly blood transfusions had a nonsignificantly smaller percentage of CFD than those transfused less often (p = 0.495). CFD+ patients had a splenectomy at a nonsignificantly younger age than CFD- patients (p = 0.36). HbE/beta thalassemia patients were not significantly less likely to develop CFD than other varieties (p = 0.50) and males had a nonsignificantly higher percentage of CFD than females (p = 0.29). This study shows CFD in thalassemia patients are still prevalent but no significant associated factors were found; however, a nonsignificantly higher prevalence of CFD was observed in patients with signs of severe disease and less efficient treatment.