Microstructures of c-axis oriented YBCO thin films made by high-pressure d.c. sputtering on LaAlO3 and MgO substrates were examined by TEM. The a-axis oriented grains, second phases and micro-twins were frequently observed in the film. The a-axis oriented grains expanded a long their c-axis directions during film growth. The a- and b-axis misorientations were observed in the film on MgO due to serious lattice mis-match between YBCO and MgO. The second phases were often accompanied with a-axis oriented grains suggesting they act as nuclei. These observed results were correlated with the measured T-c and J(c) of the films.