The microstructure of p-type (Bi,Sb)2Te3 and n-type Bi2(Te,Se)3 Peltier devices was investigated by scanning electron microscopy, energy-dispersive X-ray spectroscopy, electron probe microanalysis and transmission electron microscopy, in the bulk and close to the metal–semiconductor interface. The substitution of Sb for Bi in the p-type material varies about 1 at% or 3 × 1020 atoms cm—3 on the micrometer scale. The same behaviour was found for Se and Te in the n-type material. From these results it can be ruled out that Bi and Sb and Se and Te are statistically distributed in the crystal structure. Models for the Bi/Sb and Se/Te disorder are discussed. No evidence for the presence of antisite defects was found by electron probe microanalysis. The investigated materials were highly textured and contained large dislocation densities of 109 cm—2. In the bulk, straight dislocations, loops and half-loops were observed that are 10 nm in size. Under the electron beam elongated mobile dislocations move in the basal plane by successive hopping from pinning sites. The role of the observed extended lattice defects for accommodating local non-stoichiometry is discussed. The lattice defects might primarily affect the low-temperature electronic transport properties and the lattice heat conductivity. At the metal–Bi2Te3 interface, characteristic defect structures were identified, that extend up to between 2 and 20 μm into the Bi2Te3.