Clostridium difficile is considered to be an important causative agent of porcine neonatal diarrhoea, having taken over from classic bacterial pathogens. However, there are currently no clear data concerning the prevalence of this microorganism in piglets, or about its relative distributions among diarrhoeic and non-diarrhoeic animals. In the present study, we analyzed the presence of C. difficile in rectal swabs from 780 piglets from two age groups (newborn and 1-2-month-old pigs) by means of molecular and microbiological procedures. Furthermore DNA was isolated from the bacteria in order to identify toxin A and toxin B genes.C. difficile was not found in any of the 239 samples taken from 1- to 2-month-old pigs. Bacteria were, however, recovered from 140 out of 541 newborn piglets (25.9%), including both diarrhoeic and non-diarrhoeic animals, and animals from control farms (free of diarrhoeic animals). Genes for the production of both toxins A and B were identified in 132 of the 140 isolates (A(+)B(+)). Only seven isolates, all from the same farm and from non-diarrhoeic animals, lacked both toxin genes (A(-)B(-)), while one isolate from this same group of animals was A(-)B(+).This study provides the first report comparing the prevalence of C. difficile in large numbers of diarrhoeic and non-diarrhoeic animals. There was no clear link between bacterial isolation and neonatal porcine diarrhoea.