Lung cancer (LC) is the leading cause of cancer-related death. The sensitive and non-invasive diagnostic tools in the early stage are still poor. We present a pilot study on the early diagnosis of LC by detecting markers in exhaled breath condensate (EBC). EBC samples were collected from 105 patients with LC and 56 healthy controls. We applied chemiluminescence immunoassay to detect CEA (carcinoembryonic antigen), SCC (squamous cell carcinoma) antigen and NSE (neuron specific enolase) in EBC and serum. Concentrations of markers were compared between independent groups and subgroups. A significantly higher concentration level of each marker was found in patients with LC than healthy controls. The areas under curve of receiver operating characteristic (ROC) curves were 0.800, 0.771, 0.659, 0.679, 0.636 and 0.626 for EBC-CEA, serum-CEA, EBC-SCC, serum-SCC, EBC-NSE and serum-NSE, respectively. Markers in EBC had a higher positive rate (PR) and were more specific to histologic types than markers in serum. In addition, multivariate analysis was performed to evaluate the association of presenting markers with the stages of non-small cell lung cancer (NSCLC). EBC-CEA showed the best predictive characteristic (p < 0.006) of early-NSCLC. Our study suggested that tumor markers in EBC may have a better diagnostic performance for LC than those in serum. With further investigation on the combination of markers in EBC, detection of EBC could probably be a novel and non-invasive method to detect NSCLC earlier.