Little information is currently available regarding post-treatment outcome of TCR-targeted PCR in skin and/or peripheral blood in patients with Mycosis Fungoides (MF) when a dominant gene rearrangement is present at time of diagnosis. To address this matter, a study evaluating the correlations between post-treatment clinical, histological, blood and skin PCR data was conducted in MF patients. Twenty-seven MF patients with dominant gene rearrangement in skin lesions at time of diagnosis were selected. Peripheral blood samples were investigated as well before treatment and post treatment molecular data in skin and blood were compared with clinical and histological outcome. A dominant gene rearrangement was detected before treatment in blood of 16/25 patients. The dominant gene rearrangement disappeared from cutaneous lesions in 8/13 patients displaying complete clinical and histological response whereas skin PCR remained positive in all 10 patients with histologically persistent disease. A dominant gene rearrangement was still present in blood in 10/16 patients after treatment and blood data were not correlated with skin molecular response. This study confirms frequent detection of a dominant gene rearrangement in peripheral blood in MF patients and shows that PCR may remain positive in lesional sites even when skin lesions are successfully treated.