A short overview is given of the possibilities of electron microscopy in the determination of the local, atomic scale structure of high Tc superconducting materials. Examples include the detection of weak oxygen ordering, description and characterization of deformation modulations in layered superconductors, and analysis of very long period superstructures. The ordering principles for tetrahedral chains in Ga-, Co-, or Al-substituted YBCO are discussed and their complex defect structures are described. The incommensurate modulation in YBCO-based materials containing SO4-tetrahedra, centered on the Cu(1) sites of the CuO-chain plane, is attributed to the ordering of b-oriented SO4-rich chains in the Cu(1)-S-O layer; the structure is described in terms of an SO4-concentration wave. As examples of the new mercury-based superconducting family we discuss Y0.6Ca0.4Ba2Hg1-xMxCu2O6+y, which crystallizes in the space group P4/mmm with a = 0.3870(1) nm, c = 1.2537(1) nm. This cuprate belongs to the 1212 series; susceptibility measurements show a Tc (onset) of 90K, with a diamagnetic volume fraction of 27% at 4.2K to be reached. A second example is related to the compound Tl2HgBa4Cu2O10+y, in which ordering between single Hg layers and double Tl layers is observed.