Abstract Background Canine babesiosis, caused by Babesia canis, is a prevalent and clinically relevant disease in Europe. Severe acute babesiosis is characterized by a high mortality but prognosis is not always correlated with clinical signs nor with the level of parasitemia. Objective This study evaluated prognostic markers associated with poor outcomes in acute Babesia canis infections. Animals and Methods We compared the results of routine laboratory profiles, hand-held lactate and glucose analyzer, and the acute phase response in 2 groups of naturally infected dogs (7 survivors and 8 nonsurvivors). Samples were collected at the time of first admission and before any treatment. Subsequently, the course of prognostic markers was followed in 3 dogs experimentally inoculated with B. canis. Results Nonsurvivors showed significantly higher concentrations of lactate, triglycerides and phosphate and lower hematocrit, leukocyte counts, total serum protein concentrations, and thrombocyte counts when compared to survivors. All nonsurvivors (8/8) had hyperlactatemia, whereas most survivors (6/7) had values within the reference range. All survivors had leucocyte counts within the reference range, unlike the nonsurvivors, which showed leukopenia. During the course of acute babesiosis, the variables serum lactate, triglyceride, and phosphate concentrations, and thrombocyte count only exceeded a prognostic threshold during acute crisis. Conclusions and clinical importance Poor outcome in acute B. canis infection is indicated by changes in the laboratory profile. Intensive care should be considered for dogs presenting with moderate anemia, severe thrombocytopenia, mild to moderate leukopenia, hyperlactatemia, moderately increased serum phosphate, and triglyceride concentrations, and moderately decreased total serum protein concentrations.