Objective The objectives of this study were to assess the oral health status and parental perception of oral health needs of pediatric patients in an urban Craniofacial Center. Design This research utilized a prospective cross-sectional matched study design. The data was collected prospectively via clinical oral examinations measuring dental caries experience and gingival health status. Parental perception of oral health was assessed through a validated questionnaire. Setting The study was conducted at a Pediatric Dentistry Department and Craniofacial Center (CFC) in a large urban American city. Patients/Participants Participants were recruited and enrolled from a CFC and Pediatric Dental Clinic. Main Outcome Measure(s) The outcome measures were the oral health status and parental perception thereof. Results CFC patients’ caries experience in primary teeth was significantly lower than that of a healthy matched cohort, but statistically similar in permanent teeth. CFC patients had significantly higher unmet dental treatment needs. CFC patients had poor oral hygiene and were shown to have significantly higher plaque levels and worse gingival health than that of a healthy matched cohort. Parental perception of oral health did not show a statistically significantly difference between the two groups. Conclusions Patients in our study in an urban CFC were found to have a high unmet dental and poor oral hygiene. Despite the poor oral health status, parents of children with craniofacial anomalies did perceive their oral health as different from a matched cohort of patients without these conditions.