The objective of our case-control study was to determine whether craniofacial features on lateral nasopharyngeal radiographs (LNPRs) can predict eustachian tube dysfunction (ETD). The study included patients seen in the otolaryngology clinic from 2005 to 2011. Patients 0 to 10 years old with pressure equalization tube (PET) placement and LNPR within 6 months were included. Measurements were compared with age-matched controls selected at random to identify craniofacial features associated with ETD. Using receiver operating curve methodology, selected measurements were used to correlate age, craniofacial features, and ETD. The study population consisted of 32 patients and 34 controls. No significant differences were found between groups on any individual measurement: cranial base angle; lengths of anterior, middle, and total skull base; mandible; hard and soft palates; sella-soft-palate tip; sella-posterior nasal spine; and nasopharyngeal and palatal airway. Further statistical analysis demonstrated that patients who required PETs were more likely to have shortened anterior cranial base and maxilla relative to mandibular length. Contrary to the findings of previous studies, no single measurement was found to identify craniofacial features that may select for children with ETD requiring PETs. However, younger patients with a smaller cranial base and/or maxilla relative to mandibular length are more likely to require PETs, implying persistent ETD.