The origin of noise in YBa2Cu3O7-x (YBCO) bicrystal SQUID magnetometers on SrTiO3 substrates is investigated by comparing the microstructure of actual low-noise and high-noise devices. The most obvious difference in the microstructure is the presence of a-axis oriented particles in the high-noise devices, whereas the low-noise devices consist exclusively of c-axis oriented YBCO films. The growth of the a-axis particles in the YBCO films induces many defects, including amorphous regions, distortion in c-axis lattice planes and extra a-c interfaces. The quality of the junction boundary is also degraded by the a-axis particles. The existence of these defects are expected to affect the superconducting current and the motion of the magnetic flux in the films and hence generate extra noise in the devices.