Studies on the ontogenetic origins of human knowledge provide evidence for a small set of separable systems of core knowledge dealing with the representation of inanimate and animate objects, number and geometry. Because core knowledge systems are evolutionarily ancient, they can be investigated from a comparative perspective, making use of various animal models. In this review, I discuss evidence showing precocious abilities in non-human species to represent (i) objects that move partly or fully out of view, and their basic mechanical properties such as solidity, (ii) the cardinal and ordinal/sequential aspects of numerical cognition and rudimentary arithmetic with small numerousness, and (iii) the geometrical relationships among extended surfaces in the surrounding layout. Controlled rearing studies suggest that the abilities associated with core knowledge systems of objects, number and geometry are observed in animals in the absence (or with very reduced) experience, supporting a nativistic foundation of such cognitive mechanisms. Animal models also promise a fresh approach to the issue of the neurobiological and genetic mechanisms underlying the expression of core knowledge systems.