We investigated the effects of parasite removal on various blood clinical–chemical variables (BCCVs). BCCVs are indicators of health, reflecting, e.g., homeostasis of liver, kidney function, and bone metabolism. The study was conducted in Norway on chicks of two predatory birds: White-tailed Eagle (Haliaeetus albicilla (L., 1758)) and Northern Goshawk (Accipiter gentilis (L., 1758)). Chicks were treated against both endoparasites (internal parasites) and ectoparasites (external parasites). We treated against ectoparasites by spraying nests with pyrethrins. Within nests, chicks were randomly treated with either an antihelminthic medication (fenbendazole) or sterile water (controls). Treatment against either ectoparasites or endoparasites led to higher levels of the bone and liver enzyme alkaline phosphatase. Bilirubin levels were lower when treated against ectoparasites, whereas bile acids were higher. Anti-endoparasite treatment led to higher creatinine levels. In Northern Goshawks, treating against endoparasites led to higher urea levels and lower potassium levels. Treatment against ectoparasites increased uric acid and urea levels and reduced bilirubin levels and protein:creatinine ratios. In conclusion, anti-parasite treatments led to changes in several BCCVs, suggesting differences in nutrient absorption and physiological state of chicks that are possibly related to the costs of parasitism, but maybe also to the parasite treatment itself.