DNA analysis for early diagnosis of cervical cancer is a promising alternative for greater treatment efficiency. Biological samples obtained from the endocervix are commonly used for diagnosis, even though such samples are still little explored in the molecular context. This work aims to describe a modified protocol for extracting HPV DNA from infected endocervical cells after collection with endocervical brushes. The Wizard® Genomic DNA Purification Kit (Promega, CAT.# A1125) was used to extract DNA from endocervical samples and the extraction protocol was adapted from the manufacturer's instructions. Forty-one samples were collected from women with a mean age of 35 ± 7.8 years. It was observed that samples containing higher blood content resulted in inhibiting the amplification signal, however, all samples had enough material for DNA extraction, despite the blood contamination. The quality of the extraction was confirmed in 100% of the samples with the amplification of the actin gene, indicating that enough DNA was extracted. Considering the absorbance ratio of 260/280, the average purification of the samples was reasonably good. The protocol was able to extract and detect HPV DNA with the potential to be used in the detection of high-risk HPV from cervical brushes with a high cost-effectiveness ratio.