The maize Ac/Ds transposable element (TE) transposes by a "cut and paste" mechanism. Previous studies in maize showed that when the TE ends are in reversed orientation with respect to each other, alternative transposition reactions can occur resulting in large scale genome rearrangements including deletions and inversions. To test whether similar genome rearrangements can also occur in other plants, we studied the efficacy of such alternative transposition-mediated genome rearrangements in Arabidopsis. Here we present our analysis of 33 independent chromosome rearrangements. Transposition at the reversed ends Ds element can cause deletions over 1 Mbp, and inversions up to 2.4 Mbp in size. We identified additional rearrangements including a reciprocal translocation and a putative ring chromosome. Some of the deletions and inversions are germinally transmitted.