West Nile virus (WNV) is known to affect captive populations of alligators and, in some instances, cause significant mortalities. Alligators have been shown to amplify the virus, serve as a reservoir host, and even represent a source of infection for humans. This study describes a cutaneous manifestation of WNV in captive-reared American alligators (Alligator mississippiensis), previously described as lymphohistiocytic proliferative syndrome of alligators (LPSA), based on the findings of gross examination, histopathologic evaluation, WNV antibody testing, and WNV reverse transcriptase polymerase chain reaction (RT-PCR). Forty alligators with LPSA and 41 controls were examined. There was a significant difference (P = 0.01⁻²¹) in the WNV serostatus between the treatment group (100%) and the control group (0%, 95% CI: 0–7.3%). In the treatment group, 97.5% (39/40) (95% CI: 92.7–102.3%) of the LPSA skin lesions were positive for WNV via RT-PCR. Of the skin sections within the treatment group that had no LPSA lesions, 7.5% (3/40) (95% CI: 0–15.7%) were positive for WNV. In the control group, all of the skin samples were negative for WNV (41/41) (0%; 95% CI: 0–7.3%). The LPSA skin lesions were significantly more likely to be WNV positive by RT-PCR when compared to control animals (P = 0.07⁻²⁰) and normal skin sections from affected animals (P = 0.08⁻¹⁶). There was no significant difference in the WNV RT-PCR results between control animals and normal skin sections from affected animals (P = 0.24). These findings suggest that LPSA is a cutaneous manifestation of WNV in alligators.