Background: HER2, which is overexpressed in 25-30% of human breast cancers, is a tyrosine kinase receptor critical for the signal transduction network that regulates proliferation, migration and apoptosis of cells. Method: We report the effects of two novel HER2-binding affibody molecules (Affibody (R)), (Z(HER2:4))(2) and Z(HER2:342), on intracellular signal transduction pathways (Erk1/2, Akt and PLC 1) using quantitative immunoblotting techniques and their biological effects in cell culture. The clinically approved antibody trastuzumab (Herceptin (R)) was used as reference substance. Results: Our data showed that, although all substances target HER2, the effects on the receptor and signaling molecules differed. For example, HER2 phosphorylation was induced by trastuzumab and (Z(HER2:4))(2) but inhibited by Z(HER2:342). The effects these substances had on signal transduction correlated to some degree with changes in growth and migration, e.g. (ZHER2:4)2 stimulated phosphorylation of Erk1/2 and PLC gamma 1, as well as growth and migration, while ZHER2:342 did not. Z(HER2:342) even inhibited phosphorylation of PLC gamma 1 and migration. Conclusion: Our data suggest that Z(HER2:342) is a promising small agent (7 kDa) that may be used as an alternative, or complement, to trastuzumab. If radiolabelled, it can hopefully also be used for HER2 imaging and radionuclide therapy. Copyright (c) 2006 S. Karger AG, Basel.