The rodent whisker system has become the leading experimental paradigm for the study of active sensing. Thanks to more sophisticated behavioral paradigms, progressively better neurophysiological methods, and improved video hardware/software, there is now the prospect of defining the precise connection between the sensory apparatus and brain activity in awake, exploring animals. Achieving this ambitious goal requires quantitative, objective characterization of head and whisker kinematics. This study presents the methodology and potential uses of a new automated motion analysis routine. The program provides full quantification of head orientation and translation, as well as the angle, frequency, amplitude, and bilateral symmetry of whisking. The system operates without any need for manual tracing by the user. Quantitative comparison to whisker detection by expert humans indicates that the program's correct detection rate is at >95% even on animals with all whiskers intact. Particular attention has been paid to obtaining reliable performance under nonoptimal lighting or video conditions and at frame rates as low as 100. Variation of the zoom across time is compensated for without user intervention. The program adapts automatically to the size and shape of different species. The outcome of our testing indicates that the program can be a valuable tool in quantifying rodent sensorimotor behavior.