Protein electrophoresis provides a picture of the acute phase and humoral immune responses. While it has become more widely used in non-mammalian vertebrates and is especially sensitive in avian species, significant changes in fractions are not often observed in clinically abnormal reptiles. Capillary zone electrophoresis (CZE) is becoming more readily available for applications in veterinary laboratories. Versus traditional agarose gel electrophoresis (AGE), CZE provides greater precision and resolution. The latter can allow for the definition of additional protein fractions which may be relevant to the detection of inflammatory processes. In addition, biomarker testing options are expanding past those readily available for mammals. In reptiles, MRP-126 was previously identified as a potential biomarker in debilitated sea turtles. In the present study, CZE and MRP-126 testing was examined in clinically normal and abnormal gopher tortoises, a threatened species in the southeast United States. With CZE methodology, 7 protein fractions could be clearly identified including 3 prealbumin migrating fractions. Increases in these fractions as well as some globulin fractions were clearly observed in clinically abnormal gopher tortoises. These changes which were often marked were observed in samples that had normal or mild AGE results. Specific biomarker testing was variable in sensitivity perhaps reflective of the different health abnormalities rather than as a pan marker for inflammation. Additional studies are underway to extend these findings and examine other markers. Overall, the preliminary data suggest that these methods may have clinical and research utility in reptile species.