Objective To explore the potential risk factors of white spot lesions and follow the natural progression of white spot lesions. Methods From 2009 to 2013, eligible orthodontic patients were enrolled in Deyang Stomatological Hospital. The case group included patients who developed white spot lesions after orthodontic treatment, whereas the control group consisted of patients who did not develop white spot lesions after orthodontic treatment. Age, gender, treatment duration, toothbrushing frequency, oral hygiene level, and pre-treatment decay, missing and filled(DMF) index were collected. The areas of white spot lesions were determined by Image J shortly after orthodontic treatment and one year thereafter. Results Patients with white spot lesion had lower frequency of tooth-brushing and lower oral hygiene level than those without. Age, gender and pre-treatment DFM index were similar between the two groups. The areas of white spot lesion were decreased by 8% after one-year follow-up. However, although this difference was of statistical significance, it failed to achieve clinical significance. Conclusion Poor oral hygiene and prolonged treatment durations were significantly associated with white spot lesions. Once white spot lesions develop, the chance of spontaneous remission is low. Therefore, specific treatments are required.