Epiluminescence microscopy (ELM, skin surface microscopy, dermoscopy, dermatoscopy) is a valuable method for improving the diagnostic accuracy in pigmented skin lesions. Specific ELM criteria are already recognized for differentiating pigmented Spitz naevi (PSN) from cutaneous melanomas (CM). Our purpose was to describe the ELM appearance of a series of PSN with emphasis on PSN and CM with overlapping features. Thirty-six consecutive patients with PSN, and three cases of CM (selected from a larger database) exhibiting ELM 'spitzoid' features, were evaluated clinically, dermatoscopically and histopathologically. Most PSN (27 of 36; 75%) displayed two typical ELM patterns, namely, the starburst (19 of 36; 53%) or the globular pattern (eight of 36; 22%), which were correlated to different histopathological findings. In nine of 36 (25%) PSN, atypical ELM features which are more commonly seen in CM were observed. These PSN with an atypical pattern were characterized by an uneven distribution of colours and structures, and an irregular diffuse pigmentation resembling blue-white veil or irregular extensions (black blotches). These atypical lesions mostly occurred in children and showed no history of growth. In contrast, in three examples of CM, the typical ELM criteria of malignancy were less recognizable and either the characteristic starburst or globular pattern usually seen in PSN was present. These three lesions occurred in adults and had a recent history of change in colour, shape or size. The overlap in ELM features of some PSN and CM represents a major diagnostic pitfall when ELM examination is considered alone. In these atypical cases, clinical history including the age of the patient may be the only clue to enable a correct diagnosis.