Patients with pulmonary neoplasms have an increased risk for developing a second tumor of the lung, either at the same time or different times. It is important to determine if the second tumor represents an independent primary tumor (ie, a synchronous or a metachronous tumor, depending on whether it is present at the same time or a later time) or recurrence/metastasis, because it will significantly change the management and prognosis. Because the two tumors from the same patient are often morphologically similar, histologic examination alone may not be sufficient to distinguish between the two possibilities. We have attempted to approach this problem by microdissecting malignant cells and comparing patterns of loss of heterozygosity of multiple genes and chromosomal loci between paired tumors. We found that primary tumors of the lung and their metastasis share nearly identical patterns of loss of heterozygosity. In contrast, most synchronous and metachronous tumors as defined by the current arbitrary criteria appeared to be genetically different; therefore, they likely represented independent primary tumors. Rare synchronous tumors had similar genetic profiles, raising the possibility of recurrence/metastasis. Our data suggest that molecular analysis can help fingerprint tumors and has the potential to significantly impact management and prognosis of patients.