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In the past decade we have witnessed a rapid development in nano biotechnology that has yielded highthroughput and large-scale analysis within a miniaturized and parallel assay system. The biochip is a powerful emerging technology for biomedical, diagnostical, therapeutical, toxicological, and environmental applications. There are diverse sensing mediators used for biochips, including DNA, RNA, and protein, and moreover, even living cells are being studied. Recently, a large variety of biochip materials have been developed. Here, we will give an overview of the trends in three-dimensional biochip materials, particularly focusing on gel materials in biochip applications. We will review some unique methods and remaining challenges.