Capillary zone electrophoresis (CZE) and an immunoassay for serum amyloid A (SAA) were used to examine serum samples from clinically normal and abnormal southern white rhinoceros (Ceratotherium simum simum) and southern black rhinoceros (Diceros bicornis minor) under managed care. CZE resolved seven fractions as well as subfractions for α1 globulins. Reference intervals were calculated for white rhinoceros (n = 33) and found to have some differences over previously reported intervals generated using agarose gel electrophoresis (AGE) methods in sera from free-ranging animals. In addition, the coefficient of variation related to fraction quantitation was found to be overlapping or superior to that reported for AGE. No significant differences were observed in CZE measurands and total protein between clinically normal and abnormal rhinoceros. In contrast to CZE, significant differences in SAA levels (P < 0.001) were observed in samples from the white rhinoceros between clinically normal and abnormal animals. In addition, in limited sample sets with repeated measures, SAA provided prognostic value. Future studies should generate more robust reference intervals and delineate the application of both SAA quantitation and CZE in routine health assessments and in prognostication.