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Background  Endoparasites are considered a major health problem of South American camelids as shown in a recent survey among German and Austrian camelid owners. Although prophylactic and therapeutic measures such as application of anthelmintics are commonly used, treatment efficacy is usually not assessed. Owners have expressed significant concerns regarding the effect of antiparasitic therapy, so this study aimed to evaluate the outcome of anthelmintic treatment in German alpaca herds with different drugs.    Results  Overall, 617 samples from 538 clinically healthy alpacas > 1 year-old from 27 farms ( n  = 11–157 animals/herd) were examined. The most common parasites detected by flotation were  Eimeria  spp. (75.1%) followed by strongylids (55.0%),  Nematodirus  spp. (19.3%), cestodes (3.1%) and  Trichuris  (2.7%). After initial coproscopical examination by flotation and strongylid egg quantification by the McMaster technique, positive animals excreting at least 150 eggs per gram of faeces were included in a faecal egg count reduction test (FECRT) using fenbendazole ( n  = 71 samples), moxidectin ( n  = 71) or monepantel ( n  = 66). Pre-treatment larval cultures ( n  = 23 positive pooled farm samples) revealed  Haemonchus  (87% of the farms),  Cooperia  (43.5%),  Trichostrongylus  (21.7%),  Ostertagia  (13.0%),  Nematodirus  and  Oesophagostomum  (4.3% each). Fenbendazole treatment reduced egg excretion by 45%, moxidectin by 91% and monepantel by 96%. On the farm level, 13/18 farms that used fenbendazole, 6/6 farms that used moxidectin and 2/5 farms that used monepantel had individual FECR values < 90% (fenbendazole) or < 95% (moxidectin, monepantel).  Haemonchus  and  Cooperia  were overrepresented on the farms with reduced treatment efficacy.    Conclusions  Gastrointestinal strongylids are common in German alpacas and fenbendazole in particular was not sufficiently effective to reduce strongylid egg excretion. Although the FECRT could not unambiguously determine anthelmintic resistance in the present study, the finding that small ruminant strongylids, especially  Haemonchus , are common in alpacas indicates that determination of effective anthelmintic doses, monitoring of efficacy and adapted (selective) treatment regimens must be implemented as part of sustainable deworming practices in this species in accordance with recommendations for ruminants.

Current anthelmintic treatment is not always effective at controlling strongylid infections in German alpaca herds