Three-dimensional (3D) cell culture techniques are frequently used to model alterations in tissue architecture critically important for tumor development. Here, we report on a detailed comparison of a spheroid model of human epidermal growth factor receptor (HER2) overexpressing cancer cells with the traditional monolayer culture. In 2D culture, HER2 and HER3 form heterodimers, whereas in multicellular spheroids HER2 homodimers are formed. These homodimers localize in membrane rafts, resulting in enhanced inhibition of the proliferation of cancer cells with trastuzumab (Herceptin), a monoclonal antibody specifically targeting HER2. Within the tumor spheroids, HER2 homodimerization leads to enhanced activation of HER2 and results in a switch in signaling pathways from phosphoinositide 3-kinase (PI3K) to mitogen-activated protein kinase (MAPK). Diminished PI3K signaling is accompanied by the activation of the integrin beta4/Rac1/PAK 2 signaling cascade. We propose that the described 3D culture system may better reflect some in vivo aspects of HER signaling and can be used to further improve the understanding of the molecular mechanisms of trastuzumab action. Furthermore, the described human multicellular tumor spheroids may allow identification of new targets for the treatment of HER2-positive breast cancer patients who currently benefit suboptimally from trastuzumab treatment.