High Performance Computing (HPC) applications are data-intensive scientific software requiring significant CPU and data storage capabilities. Researchers have examined the performance of Amazon Elastic Compute Cloud (EC2) environment across several HPC benchmarks; however, an extensive HPC benchmark study and a comparison between Amazon EC2 and Windows Azure (Microsoft’s cloud computing platform), with metrics such as memory bandwidth, Input/Output (I/O) performance, and communication computational performance, are largely absent. The purpose of this study is to perform an exhaustive HPC benchmark comparison on EC2 and Windows Azure platforms. We implement existing benchmarks to evaluate and analyze performance of two public clouds spanning both IaaS and PaaS types. We use Amazon EC2 and Windows Azure as platforms for hosting HPC benchmarks with variations such as instance types, number of nodes, hardware and software. This is accomplished by running benchmarks including STREAM, IOR and NPB benchmarks on these platforms on varied number of nodes for small and medium instance types. These benchmarks measure the memory bandwidth, I/O performance, communication and computational performance. Benchmarking cloud platforms provides useful objective measures of their worthiness for HPC applications in addition to assessing their consistency and predictability in supporting them.