The method of choice for prevention and treatment of infection with Human Papillomavirus (HPV) and consequently cervical cancer is the application of prophylactic and therapeutic HPV-vaccine. The present study aimed to clone the most antigenic epitopes of the E6 antigen and to express it in E. coli at the lab-scale. The sequence of immune-bioinformatically determined epitopes of E6 was synthesized in the pGH vector. The new E6 gene was cloned into the pET28 vector by double-digestion of vector and target with NcoI and XhoI restriction enzymes. The recombinant vector was transformed into DH5α and cloned E6 gene was confirmed by colony PCR and DNA sequencing. pET28 was then extracted from DH5α and transferred into the BL21(DE3) expression host. Expression optimization was performed using various parameters. Cloning was confirmed by colony PCR and sequencing and optimized expression was performed at 25°c, IPTG=0.1 mM, OD600=1. Due to the protein production in the form of inclusion bodies and unavailability of His-Tags, the recovered protein didn’t confirm by western blot and didn’t purify by Ni-NAT affinity chromatography. This study aimed to express multi-epitope recombinant protein composed of selective E6 protein epitopes in the E. coli prokaryotic expression system to achieve an effective vaccine against HPV. The produced protein might be used as a therapeutic vaccine or as a platform for HPV detection.