The goal of this research was to develop and optimise microfluidic systems and assays for rapid detection of selected targets such as marine toxins and human IgG. The measurement of IgG, as the major format of therapeutic antibodies, was used as a prototype to develop a centrifugal-based microfluidic system for effectively monitoring biopharmaceutical production. To achieve this, a sandwich immunoassay for human IgG detection was developed and used to study the implementation of a new microfluidic CD-based cartridge. The centrifugal-based microfluidic CD adopted a serial siphon technique for implementation of automated sequential delivery of the assay reagents. Surface-confined supercritical angel fluorescence (SAF)-based detection was designed to sensitively measure the fluorescence signal from the microfluidic CDbased immunoassay. The CD substrate was functionalized with aminopropyltriethoxysilane (APTES) using plasma enhanced chemical vapour deposition (PECVD) for the immobilization of analyte capture protein. The developed prototype microfluidic system could automatically run a microfluidic assay in less than 30 min, and accurately measure industrial bioprocess samples that contained 10 mg mL1 of human IgG. Additionally, computational simulations were performed to fundamentally understand the kinetics of immunoassays in a microfluidic system. The effects of varying assay parameters on the capture of analytes in microfluidic-based heterogeneous immunoassays under real-world operating conditions, was examined by using theoretical modeling and experimental binding assay results. A marine toxin, saxitoxins (STX), was another potential target for analysis using the developed centrifugal-based microfluidic CD. Work was carried out to generate recombinant antibodies (scFv) to saxitoxin and its derivatives. After successful immunization of the host animal with different STX-conjugates, an scFv antibody phage library against antiSTX was constructed by PCR amplification of scFv genes, cloning the genes library into phagemid vector and transforming into E. coli cells. The phages expressing high affinity antibody gene were isolated by “bio-panning”.