Background: Mixed dentition is currently the stage with the highest prevalence of malocclusion, therefore, the objective was to determine the relationship of dental malocclusions in the vertical, transverse, sagittal planes with deleterious habits in pediatric patients. Methods: A cross-sectional analytical study was carried out in 155 children aged 6 to 12 years attended at the clinic of the Dentistry School of The National University of San Marcos in 2017. Results: Of the patients evaluated, 45.3% were identified with vertical malocclusion, 52.0% with sagittal malocclusion and 13.6% with transverse malocclusion. The most frequent type of malocclusion in the vertical plane was anterior deep bite (22.2%), in the transverse plane the Bis a Bis Bite (7.1%) and the Anterior Crossbite (6.5%) were less frequent. Finally, in the sagittal plane, Class II division 1 (20%) and Class III (20.7%) are frequent. Among the most common deleterious habits, anteroposition (58.7%) and mixed breathing (51.0%) were observed in contrast to the habit of retroposition, lip sucking and mouth breathing, which were the least frequent. Considering age and sex, children who have an atypical swallowing habits are more likely to have malocclusion in all three planes of space. Conclusions: It is concluded that there is an association between the deleterious habits with the different types of malocclusion in the different planes of the space, being the atypical swallowing a habit that should be diagnosed early and treated interdisciplinary.