A dissertation on various microbial analysis performed using capillary electrophoresis (CE). Four separate journal papers are presented within. The first discusses the feasibility of a CE test for measuring microbe-molecule interactions and presents for the first time experiments detailing the measurement of the binding constant of vancomycin to whole B. infantis cells using a variation of affinity capillary electrophoresis. The second is a publication discussing the theoretical models of the attainment of ultra-high efficiency peaks in capillary electrophoresis using polymer additives. Three such models are discussed within. The third is a publication on the use of microbubbles in CE for sample segregation and prevention of dispersion when using polymer based methods of microbial analysis. The last is a paper to be published presenting the work on the development of a CE method for the rapid determination of microbial contamination. The method was developed out of the need for a rapid yes/no answer to the question of contamination. The development and optimization of the system is discussed.