BackgroundCystoisospora suis is the causative agent of porcine neonatal coccidiosis, a diarrheal disease which affects suckling piglets in the first weeks of life. Detection of oocysts in the faeces of infected animals is frequently hampered by the short individual excretion period and the high fat content of faecal samples. We analysed oocyst excretion patterns of infected piglets, evaluated different detection methods for their detection limit and reproducibility, and propose a sampling scheme to improve the diagnosis of C. suis in faecal samples from the field using a protocol for reliable parasite detection.ResultsBased on a hypothesized model of the course of infection on a farm, three samplings (days of life 7–14-21 or 10–15-20) should be conducted including individual samples of piglets from each sampled litter. Samples can be examined by a modified McMaster method (lower detection limit: 333 oocysts per gram of faeces, OpG), by examining faecal smears under autofluorescence (lower detection limit: 10 OpG) or after carbol-fuchsin staining (lower detection limit: 100 OpG). Reproducibility and inter-test correlations were high with (R2 > 0.8). A correlation of oocyst excretion with diarrhoea could not be established so samples with different faecal consistencies should be taken. Pooled samples (by litter) should be comprised of several individual samples from different animals.ConclusionsSince oocyst excretion by C. suis-infected piglets is usually short the right timing and a sufficiently sensitive detection method are important for correct diagnosis. Oocyst detection in faecal smears of samples taken repeatedly is the method of choice to determine extent and intensity of infection on a farm, and autofluorescence microscopy provides by far the lowest detection limit. Other methods for oocyst detection in faeces are less sensitive and/or more labour- and cost intensive and their usefulness is restricted to specific applications.