Molybdenum disulfide (MoS₂) is a particularly interesting member of the family of two-dimensional (2D) materials due to its semiconducting and tunable electronic properties. Currently, the most reliable method for obtaining high-quality industrial scale amounts of 2D materials is chemical vapor deposition (CVD), which results in polycrystalline samples. As grain boundaries (GBs) are intrinsic defect lines within CVD-grown 2D materials, their atomic structure is of paramount importance. Here, through atomic-scale analysis of micrometer-long GBs, we show that covalently bound boundaries in 2D MoS₂ tend to be decorated by nanopores. Such boundaries occur when differently oriented MoS₂ grains merge during growth, whereas the overlap of grains leads to boundaries with bilayer areas. Our results suggest that the nanopore formation is related to stress release in areas with a high concentration of dislocation …