The aim of this study was to investigate the intra-litter infection dynamics of Isospora suis under natural conditions, and to study any association between parasite transmission and the contamination level of the farrowing pen by applying different interventions in order to reduce the transmission of I. suis infection within the litter. The study was divided in 2 trials including in total 22 litters (254 piglets). The first trial included 4 litters (where standard procedures practiced routinely on the farm piglets were applied) and the piglets were followed coprologically from farrowing until 2 weeks after weaning. The sows of those litters were also examined at various intervals before and after farrowing. The second trial included the application of 3 different management procedures: (A) standard farm hygiene and management procedures, (B) standard farm hygiene and management procedures+the first piglets found to excrete I. suis oocysts in each pen were removed from the pen, and (C) reduced cleaning. Each procedure was studied in 2 litters. This was replicated 3 times to yield a total of 18 litters. The results suggested that (i) the sow does not play an important role in transmission of I. suis in the farrowing pen; (ii) in natural infections, both the age of the piglet age at onset of oocyst excretion and the oocyst excretion patterns may vary considerably; (iii) the course of oocyst excretion or development of diarrhoea is related to the time of initial infection and (iii) piglets, which are heavy at birth, are more prone to acquire I. suis infection. Moreover, it was demonstrated that cleaning could be an effective means of restricting the spread of the parasite within the litter and thus the development of diarrhoea.