The aim of this study was to investigate the participation of Neospora caninum and Toxoplasma gondii in abortion cases of Peruvian llamas and alpacas. Fifteen aborted foetuses were recovered from two main rearing areas of camelids in Peru (Central or South Andean region). Foetal histopathology was used to detect the presence of protozoal-associated lesions in target organs. N. caninum and T. gondii infections were confirmed by immunohistochemistry (IHC) combined with PCR and by PCR alone, respectively. The influence of the species (llama and alpaca), foetal age (first, second and third gestational periods) and geographical location (Central or South Andean region) of the foetuses was also studied. Thirteen of the samples (26%, 13/50) showed lesions suggestive of protozoal infection. N. caninum infection was detected by either IHC or specific PCR in 14 out of 50 foetuses (28%), of which 8 also showed protozoal-associated lesions. T. gondii DNA was not detected in any of the foetuses analysed. Protozoal infection was more frequent in the foetuses from the second gestational period (P < 0.05, Fisher F-test). No significant association was observed between protozoal infection and species or geographical location (P > 0.05, χ2 test). The results of the present study indicate that neosporosis should be included during the differential diagnosis of abortion in llamas and alpacas. © 2007 Elsevier B.V. All rights reserved.