HPV-16 is the HPV most often linked to cervical carcinoma. E6 of the HPV-16 which expressed early incancer cells is a target for immune therapeutic methods. In the present study, after fetching the sequence ofHPV-16 E6 (accession No: ABC48950) from NCBI databank, by using hydrophilicity, flexibility, accessibility,turns, exposed surface, polarity and antigenic propensity scales, B cell epitopes of the protein were predicted. Inaddition, MHCPred version 2.0 program was used to predict MHC Class I and Class II alleles. The sequencesof the epitopes were also found out. According to this computer-based prediction the results from A0203 andDRB0101 reveal lower IC50 than other alleles. For A0203 allele, peptide with the best binding affinity was25ELQTTIHDI33. For DRB0101 allele, the peptide was 39YCKQQLLRR47. Different structural features ofthe protein were also predicted. These features were including glycosylation, kinase C phosphorylation, Caseinkinase II phosphorylation and N-myristylation sites, and disulfide bonding states. By using these computationalscales and programs, 0 glycosylation, 3 kinase C phosphorylation, 2 casein kinase II phosphorylation and 1 Nmyristylationsites and 2 disulfide bonds were predicted. Development and approval of new vaccines are keysfor control of cancer. Epitopes and structural features of proteins can be predicted and this information canhelp us in molecular and medical studies of viruses.