A large inhomogeneity of the minority lifetime from 1 to 10 μs at 77 K over the area is observed in some experiments when high-quality HgCdTe layers of the electronic type of conductivity are grown on GaAs substrates with a diameter of 76.2 mm with the (013) orientation by the method of molecular beam epitaxy. As a rule, the such lifetimes are determined by carrier recombination at Shockley-Hall-Read (SHR) centers. Modern studies and ideas about the nature of the SHR centers do not allow us to explain the observed results. The measurements of HgCdTe layers by the second harmonic generation showed the existence of a quasi-periodic change in the signal at the minima of the azimuthal dependence, which is associated with the appearance of misoriented microregions of the crystal structure. The amplitude of the quasi-periodic change in the signal decreases with increasing lifetime and completely disappears for regions with higher lifetime values. Similar dependences are observed during etching of HgCdTe layers, which indicates the existence of misoriented microregions in the bulk. Thus, misoriented microregions of the crystal structure have a significant effect on the lifetime and are new centers of Shockley-Hall-Read recombination. Keywords: HgCdTe layers, lifetime, second harmonic, azimuthal angular dependences, recombination centers, misoriented microregions.