Diagnosis of primary cutaneous T-cell lymphomas, especially of mycosis fungoides could be difficult in early stage due to clinical and histopathological similarity to reactive inflammatory dermatoses. To assess diagnostic value of complex histological, immunophenotypic and T-cell receptor gamma gene rearrangement analysis, skin biopsy specimen and peripheral blood samples of 60 patients with suspected cutaneous T-cell lymphoma were analyzed. Our results indicate clear distinction between reactive dermatoses (benign cases, n = 31) and cutaneous T-cell lymphomas (lymphoma cases, n = 17). As definite diagnosis was not obtained in a smaller group of patients (indeterminate cases, n = 12), these patients were followed up. Repeated skin biopsy confirmed mycosis fungoides in 6/12 cases, however in 6/12 patients the diagnosis remained indeterminate. We concluded that careful and complex clinical follow up and repeated histopathological, immunophenotypic and molecular analysis is needed for an appropriate diagnosis in the assessment of early stage mycosis fungoides and uncertain clinical cases.