Current biomarker measurements using benchtop analytical systems strongly suggest that real-time monitoring of the concentration of specific lipids and/or their derivatives in patient biofluids would enable physicians to more accurately track disease progression and swiftly administer therapeutic treatments. Although fluid-borne lipids constitute a severely underexplored class of biomolecules, primarily due to poor solubility in aqueous media, restrictive studies of a select few subclasses, using current bioanalytical methods, namely enzyme-linked immunosorbent assays (ELISAs), high performance liquid chromatography (HPLC) and capillary electrophoresis (CE), have afforded invaluable correlations between these analytes and a number of neuroinflammatory and neurodegenerative diseases such as Parkinson's disease, multiple sclerosis, amyotropic lateral sclerosis, atherosclerosis, lupus, and Niemann Pick type C. However, lipid analysis using benchtop ELISAs, HPLC, and CE systems in real-time has yet to be realized, because execution of these techniques require highly specialized technicians within the confines of well-equipped laboratories. Moreover, analysis times are on the order of several hours. Fortunately, the development of point-of-care medical diagnostic systems has progressed tremendously over the last decade, aggressively replacing conventional laboratory-based clinical tests with the ability to rapidly provide diagnostic information to a patient at the bedside. This technology enables faster administration of care and improved analysis of the efficacy of therapeutic methods, thus extending the duration that patients suffering from life-threatening diseases enjoy a good quality of life. This dissertation introduces a three-dimensional hybrid microfluidicanofluidic device that performs electrophoretic separations of lipid biomarkers and discusses the development of this technology into a promising alternative to current analytical methods using benchtop CE separation units. Taking advantage of a newly devised approach, non-aqueous microchip electrophoresis coupled to mass spectrometry via nanospray ionization (NAME-NSI-MS), the device successfully executes label-free characterization of lipid biomarkers in a matter of minutes. Additionally, the highly versatile architecture is compatible with in-vivo sampling methods such as microdialysis, and future iterations may incorporate additional capabilities such as sample pre-processing and analyte preconcentration. Collectively, these features constitute the invention of a powerful new medical diagnostic system with the potential to significantly improve the quality of healthcare administered to society at large.