Mycosis fungoides (MF) is the most common subtype of cutaneous T cell lymphomas (CTCLs). T cell receptor (TCR) g gene rearrangement, demonstrated by polymerase chain reaction (PCR), is the most effective method to evaluate clonality in T cell malignant neoplasms. The aim of this study was to determine whether the presence of a dominant T cell clone in the blood of stage IA and IB MF patients is associated with more severe clinical picture and/or resistance to therapy, which was previously investigated but on all stages of MF including Sézary syndrome (SS) "collectively", and to investigate the PCR outcome in the skin and blood after treatment with narrowband ultraviolet B (NB-UVB) combined with methotrexate. Thirty participants with stage I MF were included in this study. They received 36 NB-UVB sessions (3 sessions/week) in combination with methotrexate tablets 0.3 mg/kg/week for 3 months. Participants were evaluated before and after treatment regarding clinical picture, epidermotropism, density of dermal infiltrate, skin and blood examination for TCR g gene rearrangement by PCR. A dominant T cell clone was detected in the skin of 21/28 (75%) of participants and disappeared from 9/21 (42.8%) after treatment. Regarding the blood, a dominant T cell clone was detected in 14/28 (50%) of participants and disappeared from 6/14 (42.8%) after treatment. Participants were divided into 2 groups according to pre-treatment blood PCR: group I (negative) and group II (positive). Our results demonstrated that collectively, both negative post-treatment skin PCR and negative post-treatment blood PCR were significantly associated with better clinical outcome and less dense post-treatment dermal infiltrate. However, they could not show the prognostic value of pre-treatment skin or blood PCR in the prediction of post-treatment clinical and histopathological outcome.