Objective: To evaluate the prevalence of malocclusion and its association with deleterious oral habits in school going children from 9 to 11 years old, in Sakaka region of Saudi Arabia Material and Methods: The present cross- sectional study was undertaken to evaluate the prevalence of malocclusion and its association with deleterious oral habits in school going children from 9 to 11 years old, in Sakaka region of Saudi Arabia. Data were collected using a questionnaire and orthodontic examination chart. Results: 46% of the examined children had normal occlusion. Deleterious oral habits which are deemed to be the greatest culprits in the causation of occlusal discrepancies were found to be prevalent in 79.2% of the children evaluated in the study. The highest prevalence was seen for thumb sucking, which was common in more than 70% of the subjects and the lowest prevalence was for nail biting which was common in only 9% of the subjects. Conclusions: habit of mouth breathing was seen among 21% of the studied population. The variables that were most strongly associated with the presence of oral habit were malocclusion and mandibular spacing although the number of subjects with oral habits displayed more occurrence of all the variables that were under consideration. Midline shift and maxillary and mandibular crowding, illustrated in this study were higher compared to those obtained from other developing countries.