The Atlantic puffin is a medium-sized seabird with black and white plumage and orange feet. It is distributed mainly along the northern Atlantic Ocean and due, among other reasons, to human activities, it is in a threatened situation and classified as a vulnerable species according to the International Union of Conservation of Nature (IUCN). In this study, we used a total of 20 carcasses of juvenile Atlantic puffins to perform anatomical cross sections and magnetic resonance images. Thus, an adequate description of the head was made, providing valuable information that could be helpful as a diagnostic tool for veterinary clinicians, who increasingly treat these birds in zoos, rehabilitation centers and even in the wild.