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This study explores for the first time the combination of serum, urine and bronchoalveolar lavage fluid (BALF) to deep insight into the pathology of lung cancer (LC) using a metabolomic platform based on gas chromatography mass spectrometry (GC—MS). The study includes LC patients, healthy control group (HC) and a group of patients with noncancerous lung diseases (NCC) used as a control group respect to BALF because of the invasive nature this fluid collection.The metabolomic platform was applied to serum, urine and BALF samples in order to compare the metabolomic profiles of these biological fluids and establish metabolic similarities and differences between them. The application of PLS-DA presented a clear classification of groups for all types of samples, indicating the existence of altered metabolites in LC. Twenty six and thirty one perturbed metabolites in the LC were annotated in the comparison of serum and urine samples. On the other hand, sixteen metabolites were altered in BALF of LC patients compared to NCC. The pathway analysis indicated that several amino acid metabolic routes were the most affected in LC. Finally, ROC curves were applied to the dataset and metabolites with an AUC value higher than 0.75 were considered as relevant in the progression of LC.