Aims: Despite an increasing trend in Clostridium difficile infections (CDI) and high C difficile colonization rate especially among younger children. infants remain quite resistant to the disease. The goals of this study were to distinguish whether there exists a difference in CDI between children with or without diarrhoea, ascertain the prevalence of CDI, and assess CDI severity in children under 3 years with diarrhoea in our institution. Methods: A prospective study was conducted from May 2015 to June 2016. Children 3 years of age or younger were enrolled and into two groups. Every faecal sample was tested using a diagnostic two step screening algorithm including an immunochromatographic test and polymerase chain reaction. Results: The study enrolled 147 children with diarrhoea and 75 control patients. I he prevalence of CDI in children with diarrhoea was 2% (3/147), the prevalence of toxigenic C. difficile in the diarrhoeal group compared to the control group was 11.6 % (17/147) vs. 10.6% (8/75) (p < 0.9999). Conclusions: No significant difference was observed between infants with diarrhoea and the control group. We recommend not examining for C. difficile children not exhibiting specific risk factors.