The contribution is mainly focused on the formation and properties of InGaAs islands (quantum dots, QD) in a GaAs matrix, viz. a system showing properties similar to those of other materials systems. Depending on the growth techniques applied (MBE or MOCVD), the islands/dots differ in size, shape, chemical composition, and lattice strain. These parameters influence strongly the optical properties of QD structures, which might consist of single layers or complex 3-dimensional arrays. To reveal the correlation between the morphology/structure and the optical behavior of such systems different analytical methods are available, more effective in some combined applications. The present paper is mainly focused on the possibilities and limitations of transmission electron microscopy (TEM) to analyze the lattice structure of QDs down to the nm-range. Such TEM investigations imply a general problem: to deconvolute separately information on the QD size, shape (e.g., pyramidal or spherical islands), strain and composition. TEM imaging techniques used for such structural analyses will be described, including conventional diffraction contrast and high-resolution electron microscopy, respective examples of which will be presented. For the chemical analysis energy sensitive techniques (e.g., energy filtered images) are appropriate methods. Applications and limitations of such investigations will be discussed.