Clinical health checks including blood testing before brumation in fall are an important tool in reptile medicine and help to reduce the risk of complications during brumation. Electrophoresis may be useful for the evaluation of liver cell function and the detection of antigenic stimulation. The goal of this study was to compare species-specific reference intervals for plasma chemistry analytes and capillary zone electrophoresis (CZE) for a variety of pet chelonian species in fall. Lithium heparinized samples were collected from 68 clinically healthy spur-thighed tortoises (Testudo graeca), 79 red-eared sliders (Trachemys scripta elegans), and 30 map turtles (Graptemys spp.) from September to November 2016 and 2017. During the same period, 128 equivalent samples were collected from Hermann's tortoises (Testudo hermanni) and the obtained data was used for comparison. Chemistry analytes were measured from plasma using an autoanalyzer and electrophoresis was carried out by CZE. Significant variations (P < 0.0001) between the species were found for several analytes including total protein, percent albumin, and albumin: globulin ratio, α-, β-, and γ-globulin, alkaline phosphatase, glutamate dehydrogenase, alanine aminotransferase, aspartate aminotransferase, bile acids, creatine kinase, urea, uric acid, inorganic phosphorus, total calcium, and potassium. The variations in albumin (g/l) measured by CZE were also significant (P = 0.0064). No significant variations were detected for sodium levels. The results demonstrate the importance of species-specific reference intervals and provide reference intervals for the plasma chemistry and capillary zone electrophoresis in three chelonian species.