Heteroepitaxial Ge/Si(001) growth has been investigated using in situ scanning tunneling microscopy. While at 620 K the epitaxial strain is relieved by formation of three-dimensional islands (so-called ``hut'' clusters), at 690 K the strain is first relieved by hut pits, having the cluster shapes but with their apex pointing down. Although predicted theoretically to have lower energy than clusters, hut pits have never been observed individually before. Details of cluster and pit nucleation are also presented for the first time.