Objective:To explore the role of cancer stem cells (CSCs) and epithelial-mesenchymal transition (EMT) in drug resistance and metastasis of anaplastic thyroid carcinoma. Methods:Human anaplastic thyroid cancer cell line,SW1736,was sorted for side population (SP) cells which had stem cell characteristics by Fluorescent Activated Cell Sorting (FACS). Non-SP cells were treated with doxorubicin to establish drug resistant cell modes. Among SP,non-SP and non-SP drug resistant cells,the clonal formation assay was performed to evaluate the self-renewal potential;3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) cell proliferation assay was adopted to examine effects of doxorubicin on the proliferation;Genes expression of stem cell markers-nestin and ATP-binding cassette superfamily G member 2(ABCG2),the gene related to cancer resisitance and relapse-multidrug resistance gene (MDR1) and some EMT associated genes-E-Cadherin,β-catenin,vimentin,Slug and N-cadherin,were compared by performing real-time PCR. Results:SW1736 line cells contend 0.8% side population cells. Clonal formation assay revealed that SP cells displayed markedly higher clonogenic potential than non-SP cells. MTT cell proliferation assay showed that the half maximal inhibitory concentration (IC50) of non-SP drug resistant cells was obviously higher than that of non-SP cells. SP cells displayed higher genes expression of nestin,ABCG2,MDR1,slug,β-catenin,vimentin and N-cadherin,compared with non-SP cells. The gene expressions of slug and MDR1 were higher in non-SP drug resistant cells than those of non-SP cells. E-cadherin was not detected in all cell types. Conclusion: Doxorubicin can’t make the transition of non-CSCs (namely non-SP) to acquired CSCs (namely SP),but can induce the aberrant activation of EMT. SP cells may have significant impact on tumor drug resistance,recurrence and metastasis.