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Background: Allergic rhinitis is a frequent cause of nasal obstruction in the pediatric population. The effect of prolonged mouth breathing on craniofacial growth continues to be a controversial topic in the orthodontic literature. This study investigates both the role of allergic rhinitis/asthma in the etiology of posterior crossbite and ogival palate and the influence of allergic rhinitis/asthma on the long-term stability produced by transverse expansion treatment. Methods: A retrospective analysis of the clinical records of 319 subjects between 5 and 12 years, presenting for an orthodontic evaluation was performed. The sample was divided into study and control groups depending on the presence/absence of posterior crossbite and/or ogival palate. Data regarding the subjects’ breathing patterns and allergic respiratory diseases were collected. The relapse rate of transverse expansion treatment was evaluated. Results: An association (p = 0.05) was found between posterior crossbite/ogival palate and the presence of allergies. Multivariate analyses uncovered that both allergic rhinitis and younger ages were associated with posterior crossbite/ogival palate (p = 0.029890; p = 0.000283, respectively). No association was found between allergies and/or asthma and relapse following orthodontic treatment. Conclusions: Although data analysis suggests that allergies can induce transverse maxillary contraction in children, their presence did not seem to affect the outcome of orthodontic expansion treatment.