Despite the increasing use of semiconductor nanocrystals (quantum dots, QDs) with unique size-controlled optical and chemical properties in (bio)analytical detection, biosensing and fluorescence imaging and the obvious relevance of reliable values of fluorescence quantum yields for these applications, evaluated procedures for the determination of the fluorescence quantum yields (Φf) of these materials are still missing. This limits the value of literature data of QDs in comparison to common organic dyes and hampers the comparability of the performance of QDs from different sources or manufacturers. This encouraged us to investigate achievable uncertainties for the determination of Φf values of these chromophores and to illustrate common pitfalls exemplarily for differently sized water-soluble CdTe QDs. Special attention is dedicated to the colloidal nature and complicated surface chemistry of QDs thereby deriving procedures to minimize uncertainties related to these features.