During the last decade, neonatal porcine diarrhoea (NPD) has become an increased problem in Swedish herds. Clostridium (C.) perfringens type A (CpA) and C. difficile (Cd) have been highlighted as causes of NPD but their importance has also been questioned. We have previously demonstrated that CpA and Cd can be found in both diarrhoeic and healthy piglets. However, since pathogenic strains of CpA and Cd cannot be differentiated from strains found in healthy pigs and the diagnostic value of toxin-detection in stool is uncertain we have neither been able to confirm or rule them out as the cause of disease. To fill these knowledge gaps, we now want to proceed with comprehensive comparisons of CpA strains isolated from diarrhoeic and healthy piglets and evaluate if Cd-toxin can be detected in faeces from healthy piglets. This will either weaken or strengthen the association between these bacteria and NPD and generate information that can be used for the development of reliable diagnostics.