Sequence-specific double-stranded small interfering RNAs (siRNAs) may effectively silence gene expression via a mechanism called RNA interference (RNAi). The focus of this study was mainly identification of active siRNA sequences against the HER2 gene. Three anti-HER2 siRNAs that followed published algorithms were designed, cloned and then tested in the breast cancer cell line SKBR3. The silencing effects were mostly weak and contradictious when investigated by flow cytometry, western and northern techniques. The results suggested that other factors than siRNA sequence, such as target mRNA secondary structure and cell conditions, might have influenced siRNA activity, and that these are important to take into consideration when siRNAs are designed and investigated.