The purpose of the current study was to observe and correlate the characteristics of mucin balls to the ocular surface properties, and furthermore, to report the effect of different mucin balls size and number on structural alteration of the anterior cornea. The study included, two groups of patients fitted with one-month continuous, extended wear lenses for therapeutic (group 1) and optical (group 2) purposes; the later serving as a control group. Group 1 was comprised of patients with recurrent erosion syndrome, while group 2 included subjects with mild myopia and voluntary use of continuous wear lenses. The examination was performed when mucin balls were encountered during a routine visit. Clinical examination was reinforced with laser scanning in vivo confocal microscopy, which provided microstructural observations. The appearance and size of the mucin balls were described and measured at two independent time points. Qualitative analysis included shape (round, elliptical and irregular) and reflectivity (bright, homogenous and dark, heterogonous). Clinically 1460 mucin balls were encountered (822 in group 1 and 638 in group 2). The number of mucin balls analyzed by in vivo confocal microscopy was 820. Diversity was higher in group 1. The mucin balls of group 2, were more uniform - rounded in shape 81,2% and regular in reflectivity 98%. Qualitative analysis revealed a negative correlation between the size of the balls and impact on the basal epithelium morphology and also "activation" of the anterior stroma in adjacent areas. Mucin balls affect corneal surface including both epithelia disintegration as well as keratocyte "activation". The main predisposing factor for mucin ball formation appear to be the corneal surface irregularity. As structural alterations of the cornea are transient, mucin balls might be beneficial for corneal restoration due to mechanical and/or biochemical stimulation. In vivo, confocal microscopy is an innovative tool for evaluating mucin balls in their diversity and dynamics.