Layered molecular materials and especially MoS2 are already accepted as promising candidates for nanoelectronics. In contrast to the bulk material, the observed electron mobility in single-layer MoS2 is unexpectedly low. Here we reveal the occurrence of intrinsic defects in MoS2 layers, known as inversion domains, where the layer changes its direction through a line defect. The line defects are observed experimentally by atomic resolution TEM. The structures were modeled and the stability and electronic properties of the defects were calculated using quantum-mechanical calculations based on the Density-Functional Tight-Binding method. The results of these calculations indicate the occurrence of new states within the band gap of the semiconducting MoS2. The most stable non-stoichiometric defect structures are observed experimentally, one of which contains metallic Mo-Mo bonds and another one bridging S atoms.