Due to the specific size-dependent photoluminescence spectra of semiconductor nanocrystals (NCs), their use is promising as building blocks for new electronic and optical nanodevices such as light-emitting diodes, solar cells, lasers and biological sensors.(1,2) In order to design these NCs with tailored properties for specific applications, a high level of control over their synthesis is of key importance. Therefore, it is of great importance to characterise both the shape as the composition of these systems. Here, a range of different colloidal semiconductor NCs are characterised using 2D and 3D electron microscopy techniques.We will discuss, 2D semiconductor CdSe nanoplatelets (NPLs), both flat as helical shaped(3), which are investigated using electron microscopy techniques. The aim is to retrieve structural information using high resolution imaging which enables us to study the growth mechanism of these NPLs. In order to retrieve the helicity of the ultrathin helical shaped platelets, 2D electron microscopy is not sufficient as it only provides 2D images of the 3D object. Therefore, 3D electron microscopy, known as electron tomography, needs to be applied.Furthermore, heteronanocrystals (HNCs) are studied as they improve the stability and, thereby, the surface passivation of the NCs when overgrown with a shell of a second semiconductor with a higher bandgap. In this manner, the robustness of the system and the photoluminescence quantum yield of the core is increased.(4) Here, we investigate two types of CdSe/CdS core/shell HNCs: nanorods and hexagons. CdSe/CdS nanorods have attracted increasing attention because of their unique optical properties and their ability to spontaneously assemble into an organized superstructure. In order to understand the growth mechanism of these HNCs, the crystal structure should be determined and the position of the core should be located inside the shell. The presence of two types of material complicates the characterisation of the structure, hereby, electron microscopy techniques are used to retrieve both structural as elemental information. High resolution HAADF-STEM microscopy enables us to investigate the crystal structure of the core-shell nanostructure. Advanced electron tomography based on novel reconstruction algorithms(5) is used to investigate the 3D shape and to reveal the position of the CdSe core in the CdS shell.