We and others have reported that cancer side population (SP) cells have self-renewal and multidrug resistance capabilities. These phenotypes are similar to those of cancer stem cells (CSCs), cancer stem-like cells and tumor-initiating cells (TICs). It has also been reported that upregulation of the epidermal growth factor receptor (EGFR) significantly increases the number of cancer SP cells, conversely, molecular targeting of EGFR tyrosine kinases using specific kinase inhibitors downregulates CSCs. Thus, we used flow cytometric analysis and cell sorting to examine cancer SP cells in the SCA9.cl-15, WR21 and A253 cell lines that originate from a salivary gland tumor (SGT). We successfully isolated cancer SP cells from all of these cell lines. SP cells were detected following treatment of these cell lines with the receptor tyrosine kinase inhibitors (RTKIs) lapatinib, erlotinib and vandetanib. Several studies reported that RTKIs mostly reduced the SP population in cancer cells. We did not observe any detectable morphological differences between SP cells and non-SP cells. We found that the EGF RTKI lapatinib decreased the number of cancer SP cells in all cell lines investigated; however, the EGF RTKI erlotinib did not cause significant differences in the frequency of cancer SP cells in these cell lines. Addition of vandetanib significantly increased the number of cancer SP cells and upregulated the phosphorylated Akt. As far as we know, this is the first report to show that one of the RTKIs, vandetanib, can activate Akt and increase the number of cancer SP cells. It has been reported that RTKIs could competitively inhibit ABC transporters and subsequently reduced the number of SP cells. However, our observation indicated that signaling changes induced by RTKIs could even activate Akt and induce the SP population. Investigation of the SP phenotype of SGTs is important for the establishment of optimal cancer therapy.