To compare the sensitivity and specificity of DNA ploidy with cytology, human papillomavirus (HPV) testing and colposcopy in diagnosis of high-grade cervical intraepithelial neoplasia (CIN) and to assess the role of aneuploidy in cervical lesions with the worst prognosis. A prospective observational cohort study was conducted on 254 women with altered colpocytology. Colposcopy, biopsy, DNA-ICM and HPV examinations were applied to cervical cytological and histological samples. Participants were evaluated every 6 months and divided into two groups: 'Harm' and 'No-harm'. Logistic regression and multivariate COX model were used to identify independent risk factors for diagnosis and prognosis of high-grade CIN, and ROC curve to assess the sensitivity and specificity of methods. Variables 'age greater than or equal to 30 years', 'lesion size greater than 20%', 'aneuploidy' and 'HPV 16' were associated with diagnosis of high-grade CIN and 'aneuploidy' and 'women living with HIV', with a worse prognosis. Agreement for colposcopy was good, with a sensitivity of 79.3% and specificity of 94.4%; DNA-ICM and cytology were moderate, with sensitivity of 74.6% and 72.3% and specificity of 85.3% and 76.1%, respectively. High-risk HPV and HPV 16 tests were weak, with sensitivity of 75.0% and 43.75% and specificity of 50.0% and 88.64%, respectively. In relation to high-grade CIN diagnosis, DNA-ICM presented similar sensitivity and specificity to cytology and high-risk HPV test when associated with HPV 16. Regarding prognosis, this research certifies that aneuploidy is considered a predictor of more severe cervical injury.