Background Orthodontic treatment is a time-consuming and highly technique-sensitive clinical procedure. A patient's comprehension and compliance with oral hygiene instructions and appliance maintenance are critical to the success of orthodontic treatment. This study was performed to assess the knowledge, attitude and practice of patients seen at government orthodontic clinics in the Federal Territories of Kuala Lumpur and Putrajaya towards orthodontic treatment. Methods A validated, bilingual, self-administered questionnaire comprising fifteen questions across the domains of Knowledge, Attitude and Practice was used and responses were assessed with 3 responses; one correct, one incorrect and one reflecting uncertainty. 507 patients from five orthodontic centres participated in this study. Data was analysed using SPSS. Continuous data was summarised as mean and standard deviation or median and inter-quartile range, as appropriate. Categorical data was summarised as frequency and percentage, then univariable analysis was carried out with Pearson’s chi-square test or Fisher’s exact test, as appropriate. Results The mean age of respondents was 22.5 years (SD ± 2.8). A majority of respondents were female (64.1%) and from the lowest income bracket or B40 group (71%). Overall, for the knowledge domain, a majority of the respondents got all questions correct. 69.4% of patients were aware that incomplete treatment could lead to worsening of their malocclusion. 80.9% of respondents were aware of the need for a retainer upon completion of their orthodontic treatment. For the attitude section, 64.7% felt that they had to wait a very long time to see the orthodontist. In the Practice domain, the majority only got two of the five questions correct. Only 39.8% of respondents made an effort to alter dietary habits all of the time. In general, females and those with tertiary education fared better for all three domains. Conclusions The orthodontic patients in the Federal Territories of Kuala Lumpur and Putrajaya possess good knowledge about their treatment however their attitude and orthodontic related practices need to be improved.