The aim of this study was to evaluate the role of epiluminescence microscopy (ELM) in the differential diagnosis of cutaneous pigmented lesions in order to improve the detection of cutaneous malignant melanoma (CMM) at earlier stages of the disease. In total, 3865 pigmented lesions from 2121 selected patients were evaluated using ELM with a hand-held video microscope imaging system (MS 500B Micro-Scopeman, Moritex). Comparison with histology was performed on the 476 surgically excised lesions. ELM sensitivity, specificity, positive and negative predictive values as well as agreement for the different risk levels of the lesions were determined. Of the 476 cutaneous pigmented lesions removed and histologically examined, 101 (21.2%) were non-melanocytic lesions and 375 (78.8%) were melanocytic lesions. Overall agreement was 83.4% (93.1% and 80.8% for non-melanocytic and melanocytic lesions, respectively). Sensitivity and specificity of ELM in the analysis of melanocytic lesions with a pigment network were both very high (92.3% and 91.2%, respectively). Sixty new cases of CMM were identified. A high proportion of melanoma at stage AJCC IA (23 out of 32; 71.8%) was diagnosed exclusively by ELM (four of these were in situ CCM lesions). ELM is therefore a powerful tool to discriminate between melanocytic and non-melanocytic lesions in order to avoid inopportune surgical treatments for low risk lesions. Unfortunately, ELM did not show 100% sensitivity in diagnosing CMM and therefore ELM features should be integrated with data from both the history and clinical evaluation. However, ELM is much more accurate than clinical examination in detecting thin CMM.