The development of imaging devices adapted to small animals has opened the way to image-guided procedures in biomedical research. In this paper, we focus on automated procedures to study the effects of the recurrent administration of substances to the same animal over time. A dedicated system and the associated workflow have been designed to percutaneously position a needle into the abdominal organs of mice. Every step of the procedure has been automated: the camera calibration, the needle access planning, the robotized needle positioning, and the respiratory-gated needle insertion. Specific devices have been developed for the registration, the animal binding under anesthesia, and the skin puncture. Among the presented results, the system accuracy is particularly emphasized, both in vitro using gelose phantoms and in vivo by injecting substances into various abdominal organs. The study shows that robotic assistance could be routinely used in biomedical research laboratories to improve existing procedures, allowing automated accurate treatments and limited animal sacrifices.