A variety of defects in the Si/SiGe system are known to have detrimental effects on the electrical performance of metal–oxide–semiconductor field-effect transistors with strained Si channels. The ability to characterize individual defect types is therefore key for the production of high quality material. In this work we examine defects in the strained Si/SiGe system using two etching techniques and atomic force microscopy (AFM). For the first time, wavelength filtering techniques were applied to AFM images to identify non-destructively surface steps associated with misfit dislocations (MDs). Quantification of dislocation density with this method was in good agreement with results obtained from the etching techniques. The material consisted of strained Si layers on thin strain-relaxed buffers (SRBs) grown by a carbon-induced relaxation technique. Using a single etch, threading dislocations (TDs) in the strained Si layer were observed separately from those in the SRB, while pit-defects which formed in strained Si following thermal annealing could be observed and distinguished from TDs. Using a different etching technique, stacking faults (SFs) formed in supercritical thickness strained Si layers were clearly distinguished from MDs at the Si/SiGe heterointerface, enabling the density of SFs in the strained Si to be evaluated. Together with the AFM image filtering, these procedures enable a comprehensive characterization of defects in the strained Si/SiGe system. The technique is suitable for high mobility epitaxial layers, employing high Ge contents, where partially relaxed supercritical thickness layers are often necessary.