Contact lenses can induce changes in the epithelium, stroma and endothelium of the cornea, all of which can be observed clinically using the slit-lamp biomicroscope. These complications include epithelial microcysts, vacuoles and staining, stromal oedema and vascularization, and endothelial polymegethism and blebs. Each complication can be attributed to one or more aetiological factors such as hypoxia, hypercapnia, tissue acidosis, trauma, hypersensitivity and toxicity. This review outlines the way in which these complications manifest clinically, and consideration is given to management strategies and likely prognoses. Early detection of these conditions and appropriate action can usually prevent more serious ocular complications.