Objectives To characterise genotypes of Clostridium difficile strains isolated from asymptomatic individuals and patients with diarrhea. Methods Fecal specimens from 235 asymptomatic infants <12months, 76 asymptomatic children 1-11 years and 132 adult patients with antibiotic-associated and non-antibiotic-associated diarrhea obtained from Siriraj Hospital, Bangkok from October 1998 to April 1999 were examined for C difficile by cycloserine-cefoxitin-fructose agar culture. The presence of the C. difficile toxin A gene was determined by specific PCP with the use of primers 5-(CCCAATAGAAGATTCAATATTAAGCTT)-3 and 5-(GGAAGAAAAGAACTTCTGGCTCACTCAGGT)-3. All C. difficile isolates were subsequently genotyped by pulsed-field gel electrophoresis (PFGE). Results The C. difficile strains were found in 28 (11.9%) asymptomatic infants, 16 (21.1%) asymptomatic children and 33 (25%) adult patients. In total, 14 PFGE types and eight subtypes designated as types A, B, C, D, E, F, G, H, I, J, K, L, M and N, and A1, A2, A3, A4, B1, B2, B3 and E1, respectively, were identified. Only two isolates from infants and 18 isolates from adult patients were toxin A gene positive by PCP,. Both isolates of toxigenic C. difficile were from infants in the same ward and were PFGE type B. PFGE type A was the predominant type among all toxigenic isolates (12 of 18 isolates) from adult patients. The other PFGE types of toxigenic C. difficile found in adult patients were: type A1, one isolate; type B, four isolates; and type C, one isolate. Types B2 and D were identified in 38.5% and 46.2%, respectively, of the toxin A gene-negative isolates of C. difficile a from infants. Conclusions These results revealed the occurrence of three distinct clusters from different wards in Siriraj Hospital. The toxigenic C. difficile of PFGE type A and related subtypes was a predominant infective clone in adult patients, whereas non-toxigenic C. dale types B2 and D were encountered in asymptomatic infants. This information can be useful in epidemiologic investigations.