Purpose: To investigate the characteristics of the inflammatory response detected in corneas with active non-epithelial herpes simplex virus (HSV) keratitis. Materials and methods: The study was designed as a cross-sectional study undertaken at a university setting. Twenty-one eyes of 21 patients with a mean age of 40.1±13.0 years (range: 18-70 years) and whose corneal findings were compatible with active HSV keratitis were included. All patients were evaluated with in vivo confocal microscopy (Confoscan 3, Nidek). Fifty healthy, age-matched subjects served as controls. The features and extent of corneal inflammation, degree of involvement of subbasal nerve plexus and endothelial cell density were evaluated. Results: Seven eyes (33.3%) demonstrated stromal keratitis, six (28.6%) endotheliitis and eight (38.1%) presented with keratouveitis. Intraepithelial inflammatory cell infiltration, consisting of dendritic and small round cells, was observed in 11 eyes (52.4%). Stromal involvement was detected in 95.2% of eyes in the form of focal and diffuse cellular infiltrates; of these, anterior, posterior and pan stromal infiltration was observed in 85.7, 71.4 and 47.6% of cases, respectively. No particular keratic precipitate morphology was found to be diagnostic for HSV keratitis. The mean endothelial cell density of eyes with HSV keratitis (2437±599 cells/mm2) was significantly lower (-18.8%) than that of controls (3003±250 cells/mm2); (p < 0.001). The mean subbasal nerve density of patients with HSV keratitis (474.5±227.8 μm/frame) was significantly lower than that of controls (1589.6±499.0 μm/frame) (p < 0.001). Conclusions: Non-epithelial HSV keratitis related inflammatory response is characterized by cellular infiltration of all corneal layers, attenuation of the subbasal nerve plexus and endothelial cell loss. © 2012 Informa Healthcare USA, Inc.