AIM: To describe and compare corneal sensation and morphological changes of sub-basal corneal nerves by in vivo laser scanning confocal microscopy (LSCM) in herpes simplex virus (HSV) keratitis/uveitis and contralateral, clinically unaffected eyes. METHODS: A prospective clinical study included 30 HSV eyes and 30 contralateral eyes of 30 patients, diagnosed with unilateral HSV keratitis/uveitis. Both eyes underwent a complete ophthalmological examination, Cochet-Bonnet aesthesiometry and LSCM of the central cornea, using the Heidelberg Retina Tomograph III Rostock Cornea Module. After 6mo, the same examination of the HSV affected and contralateral, clinically unaffected eyes was performed. RESULTS: HSV eyes, as compared to contralateral eyes, demonstrated a significant decrease in mean corneal sensation (3.1±1.6 vs 5.3±0.8 cm), total nerve fibres number (5.7±4.4 vs 15.1±5.4), nerve branches (3.4±3.0 vs 8.4±4.7), main nerve trunks (2.3±1.6 vs 5.8±2.2), and nerve fibres density (7.5±5.6 vs 18.1±5.3 mm/mm2, P<0.05). There was no significant difference between keratitis and uveitis eyes in mean corneal sensation and nerve fibres parameters. After 6mo, corneal sensation and sub-basal nerve fibres parameters were increased significantly, but did not reach the parameters of contralateral, clinically unaffected eyes. CONCLUSION: Corneal aesthesiometry and LSCM in HSV affected eyes reveals a significant decrease of corneal sensation and sub-basal nerve fibres which recovers at 6mo but does not reach the normal level.