Background: Tracking eye position is vital for behavioral and neurophysiological investigations in systems and cognitive neuroscience. Infrared camera systems which are now available can be used for eye tracking without the need to surgically implant magnetic search coils. These systems are generally employed using rigid head fixation in monkeys, which maintains the eye in a constant position and facilitates eye tracking. New method: We investigate the use of non-rigid head fixation using a helmet that constrains only general head orientation and allows some freedom of movement. We present a MATLAB software solution to gather and process eye position data, present visual stimuli, interact with various devices, provide experimenter feedback and store data for offline analysis. Comparison with existing method: Our software solution achieves excellent timing performance due to the use of data streaming, instead of the traditionally employed data storage mode for processing analog eye position data. Results: We present behavioral data from two monkeys, demonstrating that adequate performance levels can be achieved on a simple fixation paradigm and show how performance depends on parameters such as fixation window size. Our findings suggest that non-rigid head restraint can be employed for behavioral training and testing on a variety of gaze-dependent visual paradigms, reducing the need for rigid head restraint systems for some applications. Conclusion: While developed for macaque monkey, our system of course can work equally well for applications in human eye tracking where head constraint is undesirable. (C) 2014 Published by Elsevier B.V.