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The functionalization of nanoparticles with specific receptor ligands enables their accumulation in targeted tissues and can be used therapeutically to transport drugs or for diagnostic purposes (Parveen et al., Nanomedicine 8:147-166, 2012). We could recently show that targeting endothelial cells in retinal and choroidal capillaries can be realized even under physiological conditions using quantum dots as model nanoparticles functionalized with an integrin-binding peptide (Pollinger et al., Proc Natl Acad Sci 110:6115-6120, 2013). Even though the chemistry that we used was well described in the literature and may be considered standard for the purpose, there are a number of preparation steps that are delicate and deserve special attention. It is, therefore, our intention to describe step by step the critical methods of ligand immobilization on quantum dot surfaces to facilitate the reader to reproduce our work. Here we describe the chemical modification of quantum dots with c(RGDfC) as targeting peptide that allows the resulting modified nanoparticles to adhere to endothelial cells also in the retinal tissue. We illustrate the properties of the resulting particles by showing some of the in vitro results from our previous studies. Doing so, we concomitantly encourage the reader to check particles intended for targeting cells in vivo first by extensive in vitro analysis of particle interaction with cells by the means of flow cytometry and confocal microscopy to confirm the successful functionalization. Only then the application of functionalized quantum dots into the systemic circulation of mice led to the desired localization of nanoparticles in the retinal and choroidal blood vessels (Pollinger et al., Proc Natl Acad Sci 110:6115-6120, 2013).