High altitude balloons are an effective, inexpensive and readily available conduit for conducting near space and low Reynolds number experimentation. Experiments are being developed that will use high altitude balloons as carriers for near space and low Reynolds test vehicles. The first step in developing this capability is to create a system that is able to log collected data and track and control a high altitude balloon payload. It is also beneficial that this system be flexible enough to accept different sensor types, communication methods and connection and release linkages. By combining the flexibility of microcontroller biased circuitry and the availability of commercial off the shelf products an economical design solution to this problem has been be achieved. Analysis of this system has been performed and the design has been fabricated, tested and specially modified to withstand the extreme conditions of high altitude flight.