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Plasma concentrations of PAG-1 are used for pregnancy diagnosis and as a marker of placental/foetal well-being, while those of PAG-2 may be an indicator of abortion risk in Neospora caninum-infected cows. Studies have shown that N. caninum infection modifies PAG-1 and PAG-2 patterns in maternal blood plasma. However, no prior work has examined the effects of N. caninum infection on concentrations of PAGs in foetal fluids. In this study, PAG-1, PAG-2 and pH levels were determined in the amniotic and allantoic fluids of foetuses collected at 152 days of gestation from control uninfected dams and from dams experimentally infected with N. caninum on Day 110 of gestation. Foetal fluids from infected foetuses had significantly higher PAG-2 concentrations (p = 0.026) and pH values (p = 0.02) than fluids from non-infected foetuses. In infected foetuses, significantly higher concentrations of PAG-1 (p < 0.001) and PAG-2 (p < 0.001) were detected in fluid samples showing antibodies against N. caninum than those without antibodies. Moreover, pH values were significantly higher (p = 0.011) in foetal fluid samples with antibodies than in samples from non-infected foetuses. In conclusion, this is the first report on the effect of N. caninum infection on PAG levels in foetal fluids. Our results indicate that following the experimental infection of dams with N. caninum on Day 110 of gestation, foetal fluids collected from the infected foetuses of these dams featured higher PAG-1 and PAG-2 levels and pH values than fluids from non-infected controls, provided that the samples tested showed the presence of antibodies. The clinical implications of these findings are that following infection with N. caninum, most cows will experience some level of placental damage and that this injury correlates with foetal fluid PAG levels and pH.