Introduction: To assess of the efficacy of customized lingual orthodontic system (IncognitoTM 3M Unitek), during initial aligning and Levelling based on time factor and also to assess patient‟s discomfort during initial aligning and Levelling. Methodology: 12 patients between age group of 15 – 26 years with mild to moderate crowding based on Little‟s irregularity index, in upper and lower arches which were bonded with IncognitoTM Appliance System. Results: The average rate of initial aligning and levelling for all patients is 0.0361mm/ day. When time taken for initial aligning and levelling in both the arches was compared, it was seen that time was more for maxilla than mandible but it was statistically insignificant. Conclusion: Majority of patients reported, eating and having hot drinks aggravated pain while lying down, medication, sleep and having cool drinks relieved pain. 83.33 % of patients described the overall pain experience as mild.