BackgroundPiglet diarrhoea is considered a worldwide problem resulting in animal welfare problems and financial losses for pig farmers. Porcine rotavirus and the coccidian parasite Cystoisospora suis (C. suis) are considered two important pathogens associated with diarrhoea in piglets during the suckling and early post weaning periods. To obtain an overview on the prevalence of porcine rotavirus and C. suis in piglet producing herds with solid floors and age segregated rearing, faecal sampling of 791 litters in 81 farms was performed.ResultsFor porcine rotavirus, faecal samples were analysed using a sandwich ELISA. The overall prevalence of rotavirus in the examined herds was 11.4 ± 17.7% at 2 weeks, 56.8 ± 30.7% at 4 weeks and 71.1 ± 29.1% at 6 weeks of age and the accumulated prevalence was 49, 97 and 100%. To detect C. suis, faecal samples were analysed using sedimentation. The overall prevalence of C. suis in the examined herds was 11.9 ± 15.1% at 2 weeks of age, 10.7 ± 16.7% at 4 weeks and 8.7 ± 15.3% at 6 weeks of age and the accumulated prevalence was 56, 76 and 85%. The number of empty days between farrowing batches did influence the shedding of rotavirus at 2 weeks of age but not later. Regarding C. suis, no difference in prevalence was correlated to the number of days between consecutive farrowing batches.ConclusionsOur study confirmed that rotavirus should be regarded as an ubiquitous virus that can be expected to be present in almost every pig herd in Sweden. The study also demonstrated that the number of infected litters increased from birth to 6 weeks of age. Secondly, it showed that C. suis frequently occurred in pig herds and that the number of infected litters was rather stable from two to 6 weeks of age. Consequently, both rotavirus and C. suis may play a role in intestinal disturbances in piglets during the suckling and post weaning periods despite age segregated rearing, at least in systems with solid floors. However, as this study was carried out in herds without reported problems with diarrhoea or poor weight gain, the role of these pathogens should not be overestimated.