The assimilation of computing into our daily lives is enabling the generation of data at unprecedented rates. In 2008, IDC estimated that the "digital universe" contained 486 exabytes of data [9]. The computing industry is being challenged to develop methods for the cost-effective processing of data at these large scales. The MapReduce programming model has emerged as a scalable way to perform data-intensive computations on commodity cluster computers. Hadoop is a popular open-source implementation of MapReduce. To manage storage resources across the cluster, Hadoop uses a distributed user-level filesystem. This filesystem --- HDFS --- is written in Java and designed for portability across heterogeneous hardware and software platforms. The efficiency of a Hadoop cluster depends heavily on the performance of this underlying storage system. This thesis is the first to analyze the interactions between Hadoop and storage. It describes how the user-level Hadoop filesystem, instead of efficiently capturing the full performance potential of the underlying cluster hardware, actually degrades application performance significantly. Architectural bottlenecks in the Hadoop implementation result in inefficient HDFS usage due to delays in scheduling new MapReduce tasks. Further, HDFS implicitly makes assumptions about how the underlying native platform manages storage resources, even though native filesystems and I/O schedulers vary widely in design and behavior. Methods to eliminate these bottlenecks in HDFS are proposed and evaluated both in terms of their application performance improvement and impact on the portability of the Hadoop framework. In addition to improving the performance and efficiency of the Hadoop storage system, this thesis also focuses on improving its flexibility. The goal is to allow Hadoop to coexist in cluster computers shared with a variety of other applications through the use of virtualization technology. The introduction of virtualization breaks the traditional Hadoop storage architecture, where persistent HDFS data is stored on local disks installed directly in the computation nodes. To overcome this challenge, a new flexible network-based storage architecture is proposed, along with changes to the HDFS framework. Network-based storage enables Hadoop to operate efficiently in a dynamic virtualized environment and furthers the spread of the MapReduce parallel programming model to new applications.