A microcontroller-based photon counting system has been developed by Laser and Medicine-Technology gGmbH, Berlin, Germany, in cooperation with the University of Athens. This microcontroller-based system controls, acquires, processes and stores the data from a high-resolution multichannel gas analyzer based on linear vibrational Raman scattering. The system described provides accurate photon-counting measurements using suitable photomultiplier tubes (PMT's) as detectors of the Raman signals. The implemented system amplifies, discriminates and counts the PMT pulses with a pulse-pair resolution of 5 ns. The specific implementation offers a number of important features such as portability, low power consumption, low cost, increased reliability, high sensitivity, and upgradability, and supports autocalibration and drift-compensation. Moreover, the described photon-counting system can be easily adapted to a broad field of applications, some of which are in the fields of medical electronics (confocal microscopy) and bio-electronics, air pollution measurements with Raman spectrometers, mass spectrometers, laser sounding of the atmosphere, and electro-optical systems, where photomultiplier tubes are typically used in the pulse-counting mode of operation.