Crowded pet shops can become infected with various pathogens. Although dog carriers of Clostridioides difficile tend to be asymptomatic, the toxigenic strains sometimes cause gastrointestinal symptoms in humans. The present study was conducted to determine the infection rate of C. difficile in pet shops. The feces of 137 dogs younger than one year of age, collected from four pet shops, were assessed by culture and PCR. Carriage rates of C. difficile in dogs aged ≤90, 91-180, and ≥181 day-old were 12.2% (10/82, 95% confidence interval: 6.0-21.3%), 0.0% (0/42, 95% confidence interval: 0.0-8.4%), and 7.7% (1/13, 95% confidence interval: 0.2-36.0%), respectively. Five C. difficile isolates carried genes encoding toxins A and B, while the remaining isolates contained only toxin B. However, none of the C. difficile carriers had diarrhea. These results highlight the necessity of promoting adequate hygiene precautions in pet shops to prevent infection by C. difficile.