Glass-coated amorphous wires fabricated in different production lots were examined as fundamental mode orthogonal fluxgate (FM-OFG) sensor cores. Even though those wires were meant to have the same specifications, sensor noise differed drastically depending on the wires’ production lots. Such inhomogeneity among wires will be a restriction on practical development and future mass production of the sensors. Typical M-H curves of those wires were obtained and compared, yet the result was too macroscopic and insufficient to comprehend the performance difference as sensor cores. SEM (Scanning Electron Microscopy) observations of the wires including EDS (Energy Dispersive X-ray Spectroscopy) and EBSD (Electron Back Scatter Diffraction) measurements were then performed to inspect wires from microscopic viewpoint. Notable and suggestive factors from geometrical and chemical aspects of the wires were obtained and discussed in relation to the noise performance as sensor cores. The results will contribute to achieving superior wire fabrication as well as bringing stability in quality of wires.