Field Programmable Gate Array (FPGA) devices are coming very strongly in the digital hardware systems due to the availability of ready to use resources, parallel logic operations and reconfigurable designs. The usage of FPGA systems in real time domain is also a very fruitful proposition as the FPGA devices are coming with processing cores for Real Time data processing. In a complex system scenario involving a large amount of processing tasks, there is a requirement of building the system using multiple FPGA devices. To make this possible we have to establish a real time data communication between the FPGA devices and to make it even better we have to apply data encryption techniques for making this communication secured. In this paper we demonstrate the design and implementation of a 32-bit RSA algorithms by developing suitable Hardware and Software design on Xilinx Spartan- 3E (XC3S500E-FG320) device, the implementation has been tested successfully for real time serial data communication between multiple FPGA devices using the RS232 serial interface. This development work is also useful for the embedded applications, which requires on board execution of security algorithms. The system is optimized in terms of execution speed and also has been verified using real time debugging tools. Copyright © 2011 ACM.