Ehrlichiosis is an infection caused by obligate, intracellular organisms that primarily affect cells of the immune system in dogs, cats, and people. The objective of this study was to determine the changes in the plasma lipidome profiling of dogs with canine Ehrlichiosis and try to identify potentially useful metabolic markers. Our study animals included infected (92) and healthy (17) dogs. Indirect fluorescent-antibody assay (IFA) was used for the diagnosis of Ehrlichiosis. Anorexia, depression, hemorrhagic tendencies, enlarge lymph nodes are variable clinical signs of Ehrlichia. The hemogram reflected anemia and thrombocytopenia. There were no significant changes in other biochemical parameters. The individually identified metabolites seemed to be not effective in the characterization of the canine Ehrlichiosis. However, lipid fractions lead to the hypothesis that considerable differences among diseased and healthy animals could be found in their lipidome instead of the metabolome. This reflects a great systemic energy deficit during the infection.