In summary, the lung cancer-specific methylation markers, CDO1, GSHR, HOXA11, HOXB4-1, HOXB4-2, HOXB4-3, HOXB4-4, LHX9, MIR196A1, PTGER4-1, and PTGER4-2, exhibit the potential of discriminating benign and malignant pulmonary nodules. Here, LHX9 is linked to lung cancer.