Objective: This study was conducted to determine global DNA methylation patterns in cervical cells cytologically identified as atypical squamous cells of unknown significance (ASCUS) with a normal, LSIL, or HSIL histopathological result. Methods: Methylation patterns of long interspersed nuclear elements (LINE-1) and short interspersed element (Alu) sequences were assessed using the combined bisulfite restriction analysis (COBRA) method in cervical samples with cytology-diagnosed cervical lesions. Results: In cervical precancerous lesions with hrHPV positive, the percentage of overall ( m C) and m C m C LINE-1 methylation levels showed a stepwise increase from hrHPV positive normal to HSIL with significant differences (p<0.001). However, both methylation levels were significantly higher in hrHPV negative normal than in hrHPV positive normal (p<0.001). The overall ( m C) Alu methylation in hrHPV positive LSIL and HSIL was lower than in hrHPV positive normal, with a significant difference (p<0.05). Remarkably, the percentage of u C m C and m C u C of LINE-1 and Alu in three different hrHPV positive cervical lesions showed a stepwise decrease from hrHPV positive normal, LSIL and HSIL, respectively. Furthermore, receiver operating characteristic (ROC) curve analyses revealed that the LINE-1 m C and m C m C patterns have high sensitivity and specificity for distinguishing HSIL from normal/LSIL in hrHPV positive cases at the appropriate cutoff levels. Conclusion: We have demonstrated the LINE-1 and Alu methylation data in normal and premalignant cervical epithelia. LINE-1 hypomethylation was found in hrHPV positive normal cells, with lower methylation levels associated with cancer features. In cytologically diagnosed Atypical Squamous Cells of Unknown Significance (ASCUS), the levels of m C and the m C m C pattern could be utilized in concert with hrHPV detection to classify the ASCUS sample prior to colposcopy.