Differential diagnosis of cutaneous T cell lymphoma (CTCL) and severe atopic dermatitis (AD) is often difficult because of the similarity in their skin manifestations. However, such differentiation is extremely important because of the differences in remedy and prognosis. The aim of this study was to investigate new, helpful diagnostic aids for distinguishing CTCL from AD. The frequency of forkhead box protein 3+ (FoxP3+) regulatory T cells (Tregs) in cutaneous lesions was evaluated among the three populations. Serum-soluble interleukin-2 receptor (sIL-2R), immunoglobulin (Ig)E-radioimmunosorbent test, lactate dehydrogenase (LDH) and blood eosinophil count were measured in 11 CTCL patients (including three CTCL patients misdiagnosed previously with intractable AD), 10 adult AD patients and nine psoriasis patients. The frequency of Tregs was increased significantly in cutaneous lesions of AD compared with those of CTCL. Serum IgE and LDH levels were also elevated significantly in AD compared with CTCL, whereas there were no significant differences in serum sIL-2R levels between CTCL and AD. In the three CTCL patients who were misdiagnosed with intractable AD, IgE and LDH levels were lower than in AD patients, whereas serum sIL-2R levels were as high as in AD patients and higher than in the other eight CTCL patients. The higher frequency of Tregs in the cutaneous lesions of patients with AD than in those with CTCL and higher serum IgE and LDH levels in patients with AD than in those with CTCL might be helpful reference values for the differential diagnosis of these two diseases.