The Human papillomaviruse (HPV) is a DNA tumor virus capable to transform the human epithelial cells. It has been classified in low and high risk according to its potential to induce malignant transformation. HPV is the main etiological agent involved in 99% of cervical cancer cases. This cancer is caused by two viral oncoproteins E6 and E7, which are expressed in the majority of HPV-associated carcinomas. E6 promotes deregulation of cell's cycling by binding and degrades the p53 tumor suppressor protein. The aim of this study was to clone the gene that encodes HPV-16 E6 protein in pGEM-T Easy vector thought Escherichia coli DH5-α. The E6 gene (476 pb) PCR was carried out in the Rotor Gene 3000 (Uniscience, Cobertt Research) as platform using specific primers and standard conditions. After that, amplicon was purified by commercial columns kit, inserted into pGEM vector and incorporated in E. coli DH5-α by heat-shock protocols. In order to release E6 sequence the plasmid extraction and enzymatic digestion was done and MegaBACE 750 (GE, Life Science) used to sequencing the gene. The basecalling raw data is analyzed by Sequence Analyzer (GE, Life Science) and BLASTN (NCBI) to compare the similarity of E6 gene cloned and NCBI databank. The PCR reaction resulted in single band that was purified and inserted into pGEM vector. A cleavage was done to check the presence of E6 sequence. Some samples were sequenced and the best result displayed in MegaBACE Scorecard was 636 nucleotides with 94% high qualities, supported by raw data and analyzed data in Sequence Analyzer software. Furthermore, the sequence was submitted to BLASTN obtaining the score 940; E-value 0.0; 474/474 (100%) of identify between the cloned sequence and NCBI databank. After this confirmation, it is possible to study the expression of this protein in E. coli and subclone E6 gene into yeast vector in order to compare the expression of this gene in bacterial and eukaryotic system, with objective of optimize the protein production.