Background: T-cell clonality analysis by Southern blot (TSB) in skin biopsy specimens suggestive of mycosis fungoides may be helpful in confirming the diagnosis of a cutaneous lymphoma. However, there are no data available regarding the long-term prognostic implication of such results. Objectives: We sought to determine the long-term prognostic significance of TSB results from skin biopsy specimens of patients with mycosis fungoides. Methods: We reviewed the records from the Cleveland Clinic Foundation and Northwestern University Medical Center for cases of biopsy-proven mycosis fungoides with results available for skin biopsy TSB from 1987 to 1990. Results: The detection of clonality by TSB correlates with a higher TNM stage (median stage for positive TSB, IIb vs negative TSB, Ib; P < .05), but not with age at presentation (62 vs 59 years) or duration of disease before presentation (6.2 vs 5.9 years). Although the long-term survival was not significantly different between the 2 groups, there was a trend for patients with positive TSB to die earlier (5-year survival of 67% vs 87%). Disease progression did not correlate with TSB results. Higher clonality rates were noted among patients with biopsy specimens showing a denser lymphoid infiltrate and a higher grade of cytologic atypia. Conclusions: Detection of clonality with TSB requires a significant clonal burden. Although clonality can be detected in patients with patches and plaques (T1 and T2) most cases with positive results were obtained from patients with advanced disease (T3 and T4). In our experience, detection of clonality by TSB does not correlate with disease progression and does not carry long-term prognostic implications. (J Am Acad Dermatol 2003;48:775-9.)