Abstract: Despite their evolutionary distance, the yeast retrotransposon Ty1 and retroviruses use similar strategies for replication, integration and interactions with their hosts. Here we examine the formation of circular Ty1 DNA, which is comparable to the dead-end circular products that arise during retroviral infection. Appreciable levels of circular Ty1 DNA are present with 1 long terminal repeat (LTR) and deleted circles comprising major classes, while 2 LTR circles are enriched when integration is defective. 1 LTR circles persist when homologous recombination pathways are blocked by mutation, suggesting that they result from reverse transcription. Ty1 autointegration events readily occur and many are coincident with and dependent upon DNA-flap structures that result from DNA synthesis initiated at the central polypurine tract. These results suggest that Ty1-specific mechanisms minimize copy number and raise the possibility that special DNA structures are a targeting determinant.