[Objective] To study the effect of clpE gene deletion on the virulence of Streptococcus pneumoniae. [Methods] The clpE-deficient strain was constructed by LFH-PCR and identified by PCR and sequencing. The impact of clpE mutant on the virulence of S. pneumoniae was evaluated in a mouse model. In addition, we also studied the effect of clpE mutant on adherence and invasion of host cells. Real time RT-PCR was used to measure the mRNA expression levels of autolysin A, pneumococcal surface adhesion A, pneumolysin, pneumococcal surface protein A and neuraminidase [Results] The clpE gene was replaced completely by erm cassette. Mice virulence experiments showed that the median lethal time of the wide-type was 54 h, whereas that of clpE mutant was 21d (P<0.01). Cell culture infection experiments indicated that adherence and invasion of clpE mutant were strongly reduced (P<0.05). The expression of virulent factors in clpE mutant was lower than that of the wild-type (P<0.05). [Conclusion] ClpE is involved in virulence by modulating the expressions of virulence factors.