PURPOSE: To study sub-basal corneal nerve alterations in patients with acute Acanthamoeba keratitis (AK) and fungal keratitis (FK), using laser in vivo confocal microscopy (IVCM). METHODS: A retrospective analysis of IVCM (Heidelberg Retina Tomograph 3/Rostock Cornea Module) images of 10 AK corneas and 4 FK corneas was performed, and the results compared with those of 10 normal and 12 acute herpetic keratitis (HK) corneas. Sub-basal corneal nerves were analyzed with respect to total number of nerves, main nerve trunks, branching pattern and total length of nerves per image, as well as tortuosity. For each variable, results for three frames were averaged and analyzed using analysis of variance. RESULTS: Total corneal nerve length was significantly (P < 0.0001) reduced in patients with AK (193.4 ± 124.5 μm) and FK (268.6 ± 257.4 μm) when compared with normal controls (3811.84 ± 911.4 μm). Total nerve counts in patients with AK (3.9 ± 1.2) and FK (3.6 ± 3.2) were significantly (P < 0.0001) decreased in comparison with normal controls (24.7 ± 5.5). The number of main nerve trunks and nerve branching was found to be significantly lower in AK and FK corneas, when compared with controls. There was a statistically significant decrease in the above parameters when compared with HK controls. CONCLUSIONS: The sub-basal corneal nerve plexus is significantly diminished in eyes with AK and FK, as demonstrated by IVCM. These results are more profound than previously reported findings of a diminished nerve plexus in HK.