BackgroundNeonatal coccidiosis is a common and important disease of suckling piglets in modern farming caused byCystoisospora suis. Prevalence rates are high, namely, in Portugal, although no recent data are available. The metaphylactic administration of a single dose of toltrazuril and hygienic measures are the backbone of control strategies on positive farms. However, several studies have shown that these programs are not always effective, underlining the need to revise the risk factors and control strategies currently applied. The present study evaluatedC. suisprevalence on Portuguese farms and assessed the risk factors associated with facilities and farm rearing practices.ResultsFrom the 27 tested farms, 23 were positive toCystoisopora suis(85.2%). In total, 258 litters were sampled (accounting for 516 samples—2 samples per litter), with an average of 59.7% of positive litters per positive farm. Faecal pools from litters, in which liquid faeces predominated had a higher probability of containing oocysts than litter pools with mainly solid (Odds Ratio: 9.87;p< 0.0001) or pasty faeces (OR: 7.05;p= 0.001), and samples obtained from younger animals had higher oocyst counts (coefficient: − 0.0720; 95% CI − 0.125; − 0.019). No significant effect of toltrazuril administration was observed on the positivity rate, and none of the tested farms used disinfectants with official claims against parasites and known anticoccidial effects (e.g., cresol-based products).ConclusionsTheC. suisprevalence on Portuguese swine farms appears to be similar to the prevalence found in other European countries. Repeated sampling of the same litter and the use of autofluorescence microscopy after a modified Ritchie technique seems to have increased sensitivity and consequently the detection rate of positive litters. Finally, despite the common use of oral toltrazuril,C. suiscontrol programs appear to not always be effective (based on the detection of oocysts in faecal samples), suggesting the need to revise the control strategies applied in the field, including management factors and choices of disinfectant products.