Identifying cellular and molecular differences between human and non-human primates is essential to the basic understanding of the evolution and diversity of our own species. Preserved tissues are the main source for most comparative studies between humans, chimpanzees (Pan troglodytes) and bonobos (Pan paniscus). However, these tissue samples do not fairly represent the distinctive traits of live cell behavior and are not amenable to genetic manipulation. We propose that induced pluripotent stem cells are a unique biological resource to study relevant differences between human and non-human primates, and that those differences could have potential adaptation and speciation value. To test this hypothesis, we generated induced pluripotent stem cells from chimpanzees and bonobos as new tools to explore factors that may have contributed to great ape evolution. Comparative gene expression analysis of human and non-human primate cells revealed differences in the regulation of a class of transposable elements (Long Interspersed Nuclear Element 1 or LINE1 retrotransposons) between species. Transposable elements, also known as “jumping genes”, are DNA sequences that move from one location on the genome to another via a copy and paste mechanism. A force of change in mammalian evolution, these elements have remained active during primate evolution. We revealed increased copy numbers of species-specific transposable elements in the genome of chimpanzees compared to humans, supporting the idea that there is increased transposon mobility (DNA jumping) in non-human primates in comparison to human. We propose that differences in transposon elements mobility may have differentially shaped the genomes of humans and non-human primates and could have continuing adaptive significance.