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All superconducting radio-frequency (RF) cavities are currently manufactured using high-purity Nb sheet, and although properties of the best cavities are excellent, there is still considerable variability, and we examine here the chemistry at the Nb grain boundaries (GBs), which may be a source of cavity performance degradation. Some oxidization at GBs in niobium cavities may be inevitable during the long cavity fabrication process; due to the formation of hydrosoluable niobium oxide phases during the surface removal procedure, GBs in SRF Nb can be easily attacked, resulting in the formation of uncontrolled complex niobium oxides at GBs. These GB oxide phases can significantly suppress local surface superconductivity during RF cavity operation. Thus, observation of the GB oxide structure with high-resolution transmission electron microscope (TEM) has been attempted to identify the microstructural details that affect SRF Nb cavity performance. In this paper, we developed a TEM sample preparation technique for producing damage-free SRF NB samples with good electron transparency using metallographic and focused ion beam (FIB) methods. These sample preparation techniques enabled us to successfully observe the microstructure of a variety of GBs with high-resolution TEM. TEM bright field (BF) images showed that optimized cavity surface treatment can generate impurity segregations, oxide phases, and dislocation pile-ups at the vicinity of the GBs in SRF Nb. These surface defects are predicted to be strong sources for localized degradation of surface superconductivity, and these results help explain previous magnetooptical (MO) measurements that showed early magnetic flux penetration along the GB of BCP'ed Nb bicrystal under a dc condition.