Microstructure evolution in amorphous Ge/Si multilayers grown by dual-target dc magnetron sputtering was investigated by cross-sectional transmission electron microscopy, x-ray diffraction, and growth simulations. In films grown under low intensity ion-irradiation conditions, the structure is columnar with low-density regions along column boundaries where layer intermixing was observed. By increasing the low-irradiation intensity (controlled by an applied negative substrate-bias), structures with smooth and well-defined layers could be grown. This was achieved at bias voltages between 80 and 140 V, depending on the sputtering gas pressure. As the ion-irradiation intensity is further increased, ion-induced intermixing degrades the layer interfaces and finally an amorphous Si1−xGex alloy forms. The combination of x-ray diffraction measurements and reflectivity calculations reveals an asymmetry between the Ge/Si and Si/Ge interface widths due, primarily, to a corresponding asymmetry in incident particle energies during the growth of alternate layers.