Nasopharyngeal carcinoma (NPC) often develops drug resistance following radiotherapy. The molecular basis of radiotherapy-related multidrug resistance (MDR) remains unclear. In the present study, we investigated the effect of fractionated irradiation on the expression of the MDR-1 gene and the MDR-associated protein P-glycoprotein (P-gp) in CNE1 human NPC cells. CNE1 cells were treated with fractionated X-rays. Drug resistance was determined by MTT assay. The expression levels of MDR-1 and P-gp were analyzed by RT-PCR and western blot analysis, respectively. Differential expression was analyzed by gene chips. The results revealed that low levels of mRNA expression of MDR1 were present in non-irradiated CNE1 cells. Compared with the control, the expression of MDR1 mRNA was gradually increased following fractionated irradiation. On day 21, the expression of MDR1 mRNA was increased 1.59- and 2.19-fold, compared with the control, by treatment with 10 and 20 Gy, respectively. We observed decreased MDR1 expression following treatment with 10 and 20 Gy irradiation on days 28 and 35, compared with day 21. On days 21, 28 and 35, expression was increased 1.37-, 1.40- and 1.15-fold by treatment with 20 Gy compared with 10 Gy. Expression of MDR1 was significantly upregulated by treatment with 50 Gy irradiation compared with the control on days 78 and 106. P-gp expression was consistent with that of MDR1 mRNA expression. The sensitivity of CNE1 cells to cisplatin was reduced following irradiation compared with the control. A total of 26 genes were significantly upregulated and 8 genes were significantly downregulated compared with the control. Results of the present study have shown that MDR1 and P-gp are upregulated in CNE1 cells following irradiation. Multiple genes were involved in the mechanism of radiation-induced drug resistance.