Objective: The study was performed to determine whether the human papillomavirus (HPV) genotype result from the HPV DNA chip test (HDC) was predictive of recurrent high-grade cervical intraepithelial neoplasia (CIN2-3) in patients with positive margins after a loop electrosurgical excision procedure (LEEP). Methods: A total of 184 patients with histologically confirmed CIN2-3 identified at the margin of a LEEP specimen were followed with HDC testing, hybrid capture II (HC2) analysis, and cytology examinations. Post-LEEP monitoring was conducted at 3, 6, 9, 12, 18, and 24 months during the first two years and annually thereafter. Results: Of the 184 patients, the HC2 test was positive in 179 patients (97.3%) and the HDC test was positive in 181 patients (97.6%) before the LEEP. The overall agreement between the HC2 and HDC tests was 98.9%. Forty-six (25.0%) patients developed a recurrence, and those who experienced a relapse tested positive for the same high-risk HPV genotype detected before the LEEP. Identifying the same high-risk HPV genotype by HDC testing during the follow-up period had a negative predictive value and a sensitivity of 100% in diagnosing recurrent lesions. HPV-18 was related to recurrent CIN2-3. A significant association between HPV-18 infection and recurrent CIN2-3 was found (p < 0.05). Conclusions: In patients with CIN2-3 identified at the margins of a LEEP specimen, the persistence of the same high-risk HPV infection, especially HPV-18, should be regarded as a risk factor for recurrent CIN2-3. After a LEEP, such patients require particular attention with short-term follow-up.