The expression of CK19, LUNX, and KS1/4 mRNA biomarkers was detected in the peripheral blood of non-small cell lung cancer (NSCLC) patients to investigate the feasibility of indicating lung cancer micrometastases. Micrometastases were identified in the peripheral blood of 32 NSCLC patients, 15 benign pulmonary disease (BPD) patients, and 10 healthy volunteers by reverse transcriptase-polymerase chain reaction. The detection rates of CK19, LUNX, and KS1/4 mRNA-positive cells in the peripheral blood obtained from the NSCLC group were 34.4% (11/32), 37.5% (12/32), and 25% (8/32), respectively. CK19, LUNX, and KS1/4 mRNA-positive cells were detected in 6.6% (1/15), 0.0% (0/15), and 13.3% (2/15) of the patients with BPD, respectively. However, the healthy group did not express any of the three markers. The expression of CK19, LUNX, and KS1/4 mRNA was significantly higher in the NSCLC group than that in the healthy and BPD groups (P < 0.05). CK19 and LUNX mRNA may be ideal biomarkers indicating micrometastases in patients with NSCLC; however, the diagnostic applicability of KS1/4 mRNA remains uncertain. The rate of expression of CK19 was not correlated with the clinicopathological characteristics (P > 0.05). The rate of expression of LUNX and KS1/4 was closely related to the clinical stage (P < 0.05), and not related to the clinical characteristics of the disease (age, gender, smoking history, pathological type, histologic classification, and differentiation; P > 0.05).