Pre-clinical positron emission tomography (PET) is becoming increasingly important in understanding brain physiology using animal models. One of the major challenges at present is being able to perform brain PET studies without the use of anesthesia. In most cases where the animal is minimally restrained this will require someform of motion tracking to provide the necessary temporal pose information for compensation before or during image reconstruction (eg. [1, 2]). In previous work we have demonstrated successful tracking of continuous movement in phantom studies and an anesthetized rat study in which the animal was moved manually [2]. Here we report on our first trials tracking the head of fully conscious rats moving continuously during emission and transmission PET acquisitions performed on a microPET Focus 220 scanner (SiemensPreclinical Solutions, Knoxville, USA). The motion tracking is based on a commercial stereo-optical motion tracking device called the MicronTracker Sx60 (Claron Tech. Inc., Toronto, Canada). We have previously reported in detail on this device and its suitability forsmall-scale motion tracking [3]. In this paper we (i) describe the motion tracking setup and marker considerations used for conscious animal head tracking, (ii) describe our animal handling methods,(iii) present data on motion tracker performance in the conscious animal trials, (iv) present data and observations on the character of rat movements in the imaging environment, and (v) show examples of the correction that can be obtained using these data for motion compensation.