Background: Malocclusion is highly reported among mixed dentition cases. Therefore, we aimed 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 on 155 children aged 6–12 years attended at the clinic of the School of Dentistry of Universidad Nacional Mayor de San Marcos in 2017. Results: Among 155 evaluated patients, 45.3% had vertical malocclusion, 52.0% had sagittal malocclusion and 13.6% had transverse malocclusion. The most frequent type of malocclusion in the vertical plane was anterior deep bite (22.2%), in the transverse plane, the edge-to-edge bite (7.1%) and the anterior crossbite (6.5%) were less frequent. Finally, in the sagittal plane, Class II Div 1 (20%) and Class III (20.7%) were the most 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 habit 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 malocclusions in the different planes of the space, being the atypical swallowing a habit that should be early diagnosed and treated interdisciplinary.