Network-based representations of biological data have become an important way to analyze high-throughput data. To interpret the large amount of data that is produced by different high-throughput technologies, networks offer multifaceted aspects to analyze the data. As networks represent biological relationships within their structure, it turned out to be fruitful to analyze their topology. Therefore, we developed a freely available, open source R-package called Quantitative Analysis of Complex Networks (QuACN) to meet this challenge. QuACN contains different, information-theoretic and non-information-theoretic, topological network descriptors to analyze, classify and compare biological networks.