Definition of community-onset, hospital-acquired Clostridium difficile infection (CO-HA-CDI) is difficult in patients presenting with diarrhea at hospitals or outpatient clinics, especially 4 to 12 weeks after the last discharge. We performed C. difficile stool culture for 272 diarrheic patients visiting the emergency room (ER) between January 2006 and June 2010. C. difficile was isolated from 36 cases (13.2%), and isolation rates increased year by year, from 10.1% in 2008 to 12.4% in 2009 and 16.7% in 2010. Among 32 toxin-positive isolates, 13 (40.6%) and 19 (59.4%) were associated with CO-HA-CDI and community-acquired CDI (CA-CDI), respectively, if cases with CDI diagnosed within 12 weeks after discharge were considered hospital associated. The majority (70%) of CO-HA-CDI cases occurred within 2 weeks after hospital discharge, although the interval from discharge to onset of symptoms was as long as 10 weeks. We found via tcdA and tcdB and repetitive sequence PCR analysis, that toxin A-positive/toxin B-positive isolates were the most prevalent in both CO-HA-CDI (53.8%) and CA-CDI (94.7%) cases. Toxin A-negative/toxin B-positive isolates were also still highly associated with HA-CDI cases but were also observed in CA-CDI cases. Younger age, fewer underlying diseases, lack of prior antibiotic use, and genetic diversity of isolates in repetitive sequence PCR were the main characteristics in CA-CDI cases visiting the ER.