Rationale: Our group has recently demonstrated the possibility to study microsatellite alterations of 3p in the DNA of exhaled breath condensate of NSCLC patients. Objectives: To verify whether microsatellite alterations analyzed in DNA from exhaled breath condensate reflect a profile of alterations present in tumour tissue of NSCLC. Methods: 59 subjects undergoing histological diagnosis for clinical suspicion of lung cancer entered the study: 41 resulted affected by non small cell lung cancer and 18 by non neoplastic diseases. All subjects underwent allelotyping on DNA from whole blood, exhaled breath condensate and lung tissue removed for histological diagnosis by analyzing a panel of 5 microsatellites located in chromosomal region 3p. Results obtained from DNA of the 3 biological sites and non neoplastic tissues from controls have been finally compared. Measurements and Main Results: Microsatellite alterations in DNA from tumor tissues and exhaled breath condensate of each cancer patient presented an overlappable profile of LOH and MI. A Microsatellite alterations profile comparable between DNA of lung tissue and exhaled breath condensate from controls was also confirmed. The smoking status resulted associated to the presence of microsatellite alterations in NSCLC and in controls. Conclusions: We demonstrated that microsatellite alterations in DNA from exhaled breath condensate of non small cell lung cancer patients are significantly more frequent than in control subjects. Even more interesting, the microsatellite alterations profile of DNA from exhaled breath condensate does correspond to that from lung cancer tissue of each non small cell lung cancer patient.