This study investigated the presence and abundance of Cystoisospora suis oocysts in faecal samples from 131 one- to three-week-old pig litters belonging to eight intensively raised, indoor herds in Spain. Seven herds used preventive anticoccidial toltrazuril treatments administered orally or by intramuscular injection, and one did not use preventive anticoccidial treatments. The diagnosis was performed using two oocyst flotation-concentration methods, Bailenger’s method in every herd and the more recent Joachim’s method in four herds. Oocysts were detected in every farm, the proportion of oocyst-positive samples was higher with Bailenger’s technique, and the estimated overall prevalence (95% confidence interval) was 40 (32–49)%, including 47 (29–65)% in non-medicated litters, 52 (38–67)% in orally medicated litters and 28 (16–40)% in intramuscularly medicated litters (p < 0.05). However, mixed logistic regression models indicated that the risk of infection was not significantly associated with preventive anticoccidial treatments (p > 0.05), and increased with age, was higher in herds with partially compared to fully slatted dung floors in farrowing pens and in litters with pigs with diarrhoea (p < 0.05). The median (range) oocysts per gram of faeces (OpG) in infected litters by Bailenger’s method was 623 (35–49048) and mixed negative binomial models revealed no significant association between infection intensity in positive litters and pen’s floor type and piglets age, faecal consistency and treatment status (p > 0.05). The apparent low efficacy of Toltrazuril suggests treatment administration failures, reduced residual efficacy or low susceptibility of C. suis strains in study farms and needs further investigation.