(1) Background: the popularity of rabbits has increased during the last decades and became the third common companion animals in EU. Their participation in animal assisted interventions (AAI) is growing. It is highly important to ensure the well-being of the animals in AAI. Whereas the needs and the advantages of people involved in AAI are becoming more and more evident, the needs of animals are not clearly determined, it is required not to affect the animals negatively. Those animals who are used for AAI purpose need toneed to be transported regulrarly; (2) Methods: the rabbits stress – caused by transportation – were measured by non-invasive faecaesl cortisol metabolite (FCM) analysis. 18 animals were involved in the study and experienced a 30 minutes transportation every second day duringfor two weeks (total 6 times) while 128 samples were collected; (3) Results: rabbits –could handle the transportation procedure by the first and second time but subsequently the stress hormone metabolites in faeces samples increased significantly regardless of the offered treatments (hay, carrot and apple) during the carriage. (4) Conclusions: those owners who use rabbits for Animal Assisted Intervention purpose need to take into account that transportation itself is a stressful experience for the animals.