We examined the expression levels of mRNA for multidrug resistance 1 (MDR1), multidrug resistance‐associated protein (MRP), human canalicular multispecific organic anion transporter (cMOAT), lung resistance‐related protein (LRP), topoisomerase IIα, β(Topo IIα, β) and topoisomerase I (Topo I) genes in human head and neck squamous cell carcinoma (HNSCC) specimens and mucosa (HNM) specimens, to elucidate their roles in relation to the biological characteristics and drug resistance in vivo. Fifty‐eight samples (45 head and neck carcinomas and 13 head and neck mucosa) obtained during surgical resection or biopsy from 38 patients were analyzed using the quantitative reverse transcription‐polymerase chain reaction (RT‐PCR) method. MDR1, MRP, LRP, Topo IIα, Topo IIβ, and Topo I gene transcripts were detected in all the samples tested, but cMOAT mRNA was not detected in them. Comparisons of the expression levels in HNSCC with those in HNM showed that the Topo IIα gene expression level was higher in HNSCC than in HNM (P=0.0298). Moreover, the Topo IIα mRNA level was significantly higher in metastatic lymph node samples of HNSCC than in HNM samples (P=0.0205). There were no significant differences in the six genes' expression levels between samples exposed to platinum drugs and those not exposed to platinum drugs. These results suggest that it may be effective in anticancer therapy to use topoisomerase‐targetting drugs against HNSCC, especially metastatic neck tumors, and that the expression of these genes in HNSCC is not associated with platinum drug exposure.