Background Microarray and microdissection techniques were being used for many applications to study the carcinogenesis of some human tumors. But seldom studies had hitherto combined these two techniques to study carcinogenesis mechanism of nasopharyngeal carcinoma (NPC). To identify a set of genes involved in the carcinogenesis and development of NPC, we used the microdissected homogeneous NPC tissue cells and the pure normal epithelium pillar cells to construct the whole human genome expression profiles.Methods We preserved the tissue samples from nasopharynx of 18 patients (including 13 samples of NPC and 5 samples of normal or inflammatory mucous tissue samples from nasopharynx) in RNAlater Stabilization Reagent. The tissue samples were microdissected to harvest the homogeneous tissue cells, then total RNA was isolated from them. The sufficient antisense RNA (aRNA) was amplified from these total RNA. HG-U133.Plus.2.0 GeneChip was used to construct the human whole genome expression profiling of each sample. Differential patts of expression of genes correlated with the carcinogenesis, classification and progression of NPC were identified with comparing the expression profiling data respectively in leave one out cross-validation analysis. Correlation between aRNA expression measured by the microarrays and semi-quantitative reverse transcription polymerase chain reaction (sqRT-PCR) were also ascertained, and found that hybridization results were validated in all of the 18 patients.Results Differential patts of expression of 127 genes correlated with the carcinogenesis (A P value less than 0.001 with the 2-fold differentiated expression between case group and control group) of the NPG were filtered. The top most up-regulated and down-regulated 8 genes by the way of permutation test were also selected and listed in the paper. Expression of genes E2F6 and TSPAN-1 was identified using aRNA by sqRT-PCR and showed that there was significant difference between the average value of case groups and that of control group respectively (t=2.170, df=16, P=0.045 and t=-2.946, dr=16, P=0.009).Conclusions We had identified some genes which could be the molecular marker during the carcinogenesis and the development of the NPC. The genes which selected from the different subgroups seemed to be implicated for the diagnosis,classification, and progression of NPC, and provided important insights into their underlying biology.