Few studies have investigated the changes of Th1- and Th2-type cytokines in pulmonary embolism (PE) patients. In this study, the gene expression of interleukins and the balance of Th1- and Th2-type cytokines in the peripheral blood mononuclear cells (PBMCs) of PE patients and controls were investigated. A total of 20 PE patients and 20 gender- and age-matched controls were included in the study. Human cDNA microarray analysis was used to detect the differences in cytokine gene expression between the two groups and a random variance model corrected t-test was used to analyze the statistical data. In comparison with the controls, 12 genes were found to be downregulated, specifically IL1A, IL9, IL17B, IL19, IL23A, IL25 (p<0.05), IL2, IL3, IL13, IL22, IL24 and IL31 (p<0.01), and 2 genes were found to be upregulated, specifically IL10 and IL28A, in the PE patients. The expression levels of IFN-γ and IL2 mRNA in the PE patients were significantly lower than those in the control group (p<0.01), while the IL20 mRNA expression levels were significantly upregulated (p<0.01). We conclude that there are significant differences in interleukin gene expression between the PE patients and the control group. A shift of the Th1/Th2 balance comprising enhanced Th2 activity and reduced Th1 activity in the PE patients is also demonstrated.