The expression of CD44 standard form (CD44s) and variant isoforms v3 and v6 was analyzed in 233 resected non-small cell lung carcinoma (NSCLC) specimens by immunohistochemistry (IHC), and the mRNA status of CD44v3 and CD44v6 in a cohort of samples was determined by in situ hybridization (ISH) and further confirmed by reverse transcriptase polymerase chain reaction (RT-PCR). The expression of CD44s, CD44v3, and CD44v6 was correlated with clinicopathologic variables and survival. The expression of CD44v3 and v6 was reduced in 97% and 90% of the adenocarcinomas and in 86% and 74% of the large cell/anaplastic carcinomas, respectively, as compared with squamous cell carcinomas, where they were reduced in 53% and 51% of the cases (P = .0001 and P = .004 for v3 and v6). The corresponding values for CD44s were 92%, 70%, and 51%, respectively (P = .011). The reduced CD44s and CD44v6 expression was associated with lymph node metastases (P = .03 and P = .005, respectively) and the reduced expression of CD44s also with advanced stage (P = .04). Recurrences during the follow-up were more often found within the tumors showing reduced expression of CD44v3 (P = .04). Combining ISH and IHC results showed that CD44v3 and v6 mRNA were not always processed into protein, suggesting a regulation disturbance posttranscriptionally since malignant transformation of cells has occurred. In survival analyses, the reduced expression of CD44s and CD44v3 was associated with a shortened disease-free survival (P = .04 and P = .01, respectively). In multivariate analysis, CD44v3 retained its independent prognostic value (P = .03). These results emphasize the value of CD44, and especially the v3 variant isoform in the behavior of NSCLC.