RNA interference has become a powerful tool for specific inhibition of gene expression in mammalian cells. Expression constructs allow for the long-term delivery of short interfering RNAs, usually through the expression of Pol III-transcribed hairpins. In some instances, these expression systems have been shown to have side effects, including induction of the interferon response and cytotoxicity. Here we demonstrate that H1-expressed hairpins, as well as the cloning vector, reduce the plating efficiency of HeLa cells. This toxicity is abrogated by coexpression of the hairpin in the same transcript as a human Alu repetitive element. These Alu-linked hairpins retain the ability to knock down expression of target mRNAs. This modification, which we term SINE (short interspersed repetitive element)-enhanced short hairpin RNA, provides an alternative expression system for hairpins with reduced side effects.