Tropheryma whipplei has been hypothesized to be able to cause diarrhoea, but data from young children are scarce. In this hospital-based case-control study 534 stool samples of children aging between 2 months and 15 years from rural Ghana were analysed for the presence of T.whipplei. Overall stool prevalence of T.whipplei was high (27.5%). Although there was no difference in T.whipplei carriage overall between cases and controls, cases aging 0-12 months carried T.whipplei in their stool twice as often than controls without diarrhoea. The results from this study may support the hypothesis that T.whipplei can cause diarrhoea in first-time infection.