Antigenic group 2 coronavirus was detected in a fecal sample of an adult alpaca by reverse transcription-PCR. The presence of alpaca coronavirus (Ap. CoV) in the small intestine was demonstrated by immune histochemistry with an antinucleocapsid monoclonal antibody that reacts with group 2 coronaviruses. Other common causes of diarrhea in adult camelids were not detected. We conclude that nutritional stress may have predisposed the alpaca to severe Ap. CoV infection. Copyright ยฉ 2008, American Society for Microbiology.