In the present study, follicle-sinus complexes (FSCs) were harvested from the muzzle skin of 123 dogs with suspected canine rabies, and the sensitivity and specificity of FSC analysis were compared with those of brain tissue immunohistochemistry analysis. In the FSCs, viral antigen was detected from Merkel cells. Sensitivity was 97.3%, specificity was 100%, and the coefficient κ was 0.88. These results reconfirm that FSCs are very useful for the postmortem diagnosis of canine rabies, and suggest that 5 FSCs can yield results that are almost equivalent to those derived from brain tissue analysis in rabid dogs.