In competitive sports, the use of autologous blood transfusion has been identified as a prohibited practice, but remains as one of the most difficult doping practices to detect. Although the implementation of the Athlete’s Biological Passport can be effective in detecting such doping, the process is time-consuming and the analyses rely on variations in number of biological markers, which is an indirect approach to the detection. I explored to directly detect an autologous blood transfusion via capillary electrophoresis. Capillary electrophoresis is an effective tool for the analysis of biological analytes with advantages of faster separation time, high efficiencies, and low sample consumption. Multiple parameters in the capillary electrophoretic separations were manipulated in search of complete separation of fresh and aged red blood cells. By changing the length of the capillary from 40 cm to 60 cm, changing the separation buffer’s pH to 3.0 and 4.0, and applying a counter pressure into the separation to accentuate the mobility differences of the fresh and the aged red blood cells. However, for longer capillary separation, despite the successful separation of red blood cells with peaks further spread apart, distinction between the fresh and the aged red blood cells was not clear. Mobility of the red blood cells at low pH was not strong enough to pass through the detector. And lastly, pressure applied separation displayed variable results influenced by number of factors such as drag force influencing the red blood cell based on its orientations. However, such conclusion cannot be made without further investigation. Fluorination of capillary effectively created the inner surface that could suppress electroosmotic flow in a very stable and reproducible manner. Fluorinated capillary was effective at separating a sample mixture containing various cationic and neutral proteins. In the process, I discovered that the fluorinated surface adsorbs analytes due to its hydrophobic nature. Also, the fluoride-silicon bond inside the capillary, once formed, may be irreversible. Separation of red blood cells using the fluorinated capillary did not result in RBC passing through the detector due to adsorptions and the lack of mobility.