Abstract: This dissertation explores methods of using MEMS technology to develop tools for the large-scale high-throughput analysis of genetic variation and function in the area of genomics and proteomics. It is divided into two parts. Part I reports the design and fabrication of a silicon micromachined pin that serves as a novel contact-printing device. Part II report the use of shape-encoded particle (SEP) for large-scale genetic analysis. Part I reports the use of MEMS technology to design and fabricate an improved contact printing pin which has potential application in the DNA/Protein microarray for small and precise droplet printing onto a solid support. We have demonstrated the viability of silicon microarray pins, taking advantage of lithographic and batch processing of silicon micromachining in comparison with conventional and serial processing currently used by commercial pins. Reduction in spot size (< 50% in diameter, i.e. > 4X in array density), elimination of pre-printing, and 5X increase in spots printed per run are achieved. Wettability of pins are controlled using selective surface treatment. Our goal is to provide an economic solution for better accuracy and repeatability in DNA and protein printing. Part II reports the use of a shape-encoded particle (SEP) as a substrate for biochemical probe (such as DNA or protein) attachment and identification. Its application involves large-scale genomic/proteomic analysis of multiple data based on shape-recognizable microparticles. Our goal is to provide a simple tool to greatly simplify the DNA microarray procedure, and allow more flexibility and better quality control in experimental design. Compared to other bar-coding techniques, SEPs have advantages of simple fabrication, low cost, unlimited supply of distinguishable particles, and non-interfering with the reporter signals. We have successfully demonstrated the use of shape encoded particles in SNP genotyping. The particles have been coupled to DNA oligo probes and hybridized to fluorescently label complementary targets. The particles are self-assembled by particle-trapping mechanism on surface. The hybridization products are read by fluorescent scanners, and the images are decoded and analyzed by shape analyzing software. Thus, complete system integration has been achieved.