The objective of this study was to investigate whether digital surface microscopy (DSM) could be used for the follow-up and comparison of malignant and benign conjunctival pigmented lesions (CPLs). Thirty-nine CPLs [16 de novo malignant melanomas (MMs), one MM arising from primary acquired melanosis (PAM), six PAMs and 16 naevi] were digitally analysed and biopsied. All of the PAMs and 10 naevi, which had not been surgically excised, were followed up using DSM. Thirty parameters were evaluated grouped into four categories: geometry, colour, texture and islands of colour. None of the CPLs that were followed up, which comprised 10 naevocytic naevi and seven PAMs, showed any morphological change at DSM analysis, except for one PAM which developed an MM 1 year later. Of the geometric variables examined, the area, maximum diameter and minimum diameter showed significantly higher values in MMs compared with benign CPLs. With regard to the colour of CPLs, MMs were significantly darker and bluer than naevi. In the texture group, contrast was significantly higher in MMs. In the islands-of-colour group, the imbalance of blue-grey regions and the presence of dark areas were significantly higher in MMs. DSM greatly simplified the follow-up of CPLs, such as PAMs with atypia, by providing satisfactory quality images with high reproducibility; this technique is also easy to use and well accepted by patients. Moreover, this preliminary study allowed us to determine which objective variables could be important for distinguishing between benign CPLs and conjunctival MMs.