Background The relationship between apoptosis and tumors is a major focus in cancer research. RNA interference (RNAi) technology has emerged as a very potent tool to generate cellular knockdown phenotypes of a desired gene. The aim of this study was to explore the effect of siRNA specific to the protein casein kinase 2 alpha (CK2 alpha) on apoptosis of laryngeal carcinoma cells and to explore possible mechanisms. Methods An siRNA expression plasmid specific to CK2 alpha, psiRNA-hH1neo-CK2 alpha, and a non-specific siRNA expression plasmid, psiRNA-hH1neo-cont, were constructed and transfected into Hep-2 cells by a lipofectamine method. The mRNA and protein levels of CK2 alpha in transfected cells were determined by reverse transcription-polymerase chain reaction (RT-PCR) and Western blotting analysis. Apoptosis was measured by Annexin V-fluorescein isothiocyanate (FITC)/propidium iodide (PI) double-staining methods. The morphological changes to Hep-2 cells were observed under transmission electron microscopy (TEM). The levels of Bcl-2 and Bax proteins were measured by Western blotting analysis. Results Levels of CK2 alpha mRNA and protein were significantly decreased in the psiRNA-hH1neo-CK2 alpha group compared to the other groups (P<0.05). The apoptotic rate of the psiRNA-hH1neo-CK2 alpha transfected group was significantly higher compared to that in the untransfected group and the siRNA-hH1neo-cont transfected group (25.66%+/- 0.83%, 3.66%+/- 0.43%, and 5.18%+/- 0.22%) (P<0.05). Compared with the untransfected group and the siRNA-hH1neo-cont transfected group, the psiRNA-hH1neo-CK2 alpha transfected group presented with classical ultrastructural features of apoptosis, such as karyopyknosis, chromatic agglutination adjacent to the nuclear membrane, and apoptotic bodies. Compared with the other two groups, the level of Bcl-2 protein in the psiRNA-hH1neo-CK2 alpha transfected group was decreased (0.20 +/- 0.09 vs. 0.72 +/- 0.16, 0.56 +/- 0.11, P<0.01), while the Bax protein level was increased (0.81 +/- 0.17 vs. 0.26 +/- 0.12, 0.33 +/- 0.17, P<0.01) and the ratio of Bcl-2 to Bax was decreased (0.25 +/- 0.05 vs. 2.76 +/- 0.21, 1.70 +/- 0.22, P<0.01). Conclusions The siRNA expression plasmid specific to CK2 alpha could suppress CK2 alpha expression and induce the apoptosis of laryngeal carcinoma cells. This is possibly by decreasing the Bcl-2/Bax ratio. CK2 alpha may provide a potential therapeutic target against human laryngeal carcinoma. Chin Med J 2012;125(9):1581-1585