Piglet isosporosis is one of the most common parasitic diseases in modern pig production. To prevent clinical disease, prophylactic treatment of piglets with toltrazuril (BAYCOX® 5%, Bayer HealthCare, Animal Health, Monheim, Germany) is widely practiced in the past 20 years. There are only very few reports documenting the likely effect of managerial practices, such as hygiene measures, all-in-all-out management of farrowing facilities and piglet manipulations, and/or farm-specific environment - i.e. design and materials of the farrowing pen and room - in the risk of disease occurrence and transmission. Therefore, in this cross-sectional study, we identified litter- and herd-level factors associated with the odds and the level of Isospora suis oocyst excretion in nursing piglets of Greek farrow-to-finish pig herds. Faecal samples were collected from 314 liters of 55 randomly selected herds. Oocyst counts were determined by a modified McMaster technique and possible risk-factor data were collected through a questionnaire. In the analysis, we employed a two-part model that simultaneously assessed the odds and the level of oocyst excretion.