The apicomplexan protozoans of the genera Hepatozoon and Babesia are emerging parasite pathogens most prevalent in canines in the Brazil. Although diagnostic definitive is based on molecular analysis, morphological findings and the quantitative hematological aspects are crucial for diagnosis and staging those parasitic diseases. Thus, we evaluated the hematological profile of canines naturally infected by Babesia spp. and Hepatozoon spp. through a retrospective study with 452 dogs diagnosed by blood smear. Clinical findings and population data were determined from the review of medical records. The hematological aspects of 124 dogs with Babesia spp. and 328 with Hepatozoon spp. young dogs, less than 1 year old and females were commonly affected by both diseases. In animals with Babesia spp., the most observed hematological alterations were anemia (83.87%), normocytic normochromic type (37.9%), leukopenia (45.16%), neutropenia (28.22%), lymphopenia (44.35%), eosinopenia (71.77%), monocytopenia (29.03%), and thrombocytopenia (86.03%). In animals infected with Hepatozoon spp. were anemia (76.52%), normocytic normochromic type (49.69%), leukocytosis (26.22%), neutrophilia (30.49%), lymphopenia (29.57%), eosinopenia (40.55%), monocytopenia (21.04%), and thrombocytopenia (54.27%). This study highlights the importance of epidemiological care, especially with the puppies, keeping them free from disease vectors and reinforces the importance of the blood count in the diagnosis, treatment, and prognosis of these diseases. © 2022, The Author(s), under exclusive licence to Springer-Verlag London Ltd., part of Springer Nature.