Aims Pneumococcal infections are a major public health problem, especially in developing countries, and the current pneumococcal vaccines do not cover all pathogenic strains. New, more economical serotype-independent vaccines based on species-common protein antigens are being pursued. The pneumococcal whole-cell vaccine which is based on noncapsular antigens common to all strains induces serotype-independent immunity. In the present study, we developed a new candidate for a whole-cell pneumococcal vaccine in which two important virulence factors, the capsule and pneumolysin, were deleted. Methods and Results Conclusions Protection was elicited by immunization against colonization in mice with a killed mutant strain and the antibody response in the mice serum was evaluated. This candidate vaccine was effective in preventing nasopharyngeal colonization. The mice immunized with this candidate vaccine had significantly higher serum antibody titres than mice that received the adjuvant alone. Based on obtained results in this study, the engineered whole-cell pneumococci can be considered as a vaccine candidate in future studies. Significance and Impact of the Study This candidate vaccine can overcome the limitations of available polysaccharide vaccines.