Embedded medical devices, such as wearable devices, are becoming increasingly common, but data from these devices is both very private and highly vulnerable to theft. Data needs to be collected from multiple devices to improve the effectiveness of treatment. The medical devices, data processing sites and intended care givers are often geographically distributed, and operate on different time scales with collected data being aggregated for days or months before analysis and usage. Current approaches to data security do not provide a framework for end-to-end protection, where data can always be encrypted but still used effectively. We present a security architecture with end-to-end encryption that supports 1) secure collection of data from embedded medical devices, 2) protected computing on this data in low-cost commodity cloud environment and 3) restricts the delegation of access to this data to designated recipients. The basis of the architecture comes from recent advances in lattice encryption technologies. This approach leverages recent breakthroughs in Homomorphic Encryption (HE) and Proxy Re-Encryption (PRE) that would practically support specific data aggregation, processing and distribution needs of a secure medical data architecture. This architecture lowers health care data system costs by securely outsourcing computation to cloud computing environments while simultaneously reducing vulnerabilities to some of the most problematic security challenges such as insider attacks and enables additional cost savings with lower-cost embedded medical devices.