New strategies for integrating sample pretreatment with chemical analyses under a single format is required for rapid, sensitive and enantioselective analyses of low abundance metabolites in complex biological samples. Capillary electrophoresis (CE) offers a unique environment for controlling analyte/reagent band dispersion and electromigration properties using a discontinuous electrolyte system allowing for highly efficient separations to be achieved. A fundamental study of the thermodynamic and electrokinetic parameters influencing enantioselectivity in chiral CE separation is first examined. A new strategy for single-step analysis of low abundance metabolites via online sample preconcentration with chemical derivatization by CE (SPCD-CE) is then detailed within. In-capillary sample preconcentration serves to enhance concentration sensitivity via electrokinetic focusing of long sample injection volumes for lower detection limits, whereas chemical derivatization by zone passing of single or multiple reagents is used to expand detectability and selectivity, notably for enantiomeric resolution of metabolites lacking intrinsic chromophores. Together, on-line SPCD-CE can provide over a 100-fold improvement in concentration sensitivity, shorter total analysis times, reduced sample handling and improved reliability for a variety of biologically relevant amino acid and amino sugar metabolites, which is also amenable to automated high-throughput screening. The basic method development and optimization parameters relevant to SPCD-CE, including applications to bacterial metabolite flux and biomarker analyses are discussed. Insight into the mechanism of analyte focusing and labelling during electromigration by SPCD-CE is also presented, as well as future directions for continued research using this unique integrated analytical platform. / Thesis / Doctor of Philosophy (PhD)