► We applied the MIQE guidelines to clinical and pre-clinical trials. ► We proposed a solution to handle many samples, keeping the MIQE compliance close to 100%. ► The bench side quality measurement in these trials was also part of this work. The “Minimum Information for the Publication of qPCR Experiments” (MIQE 3) guidelines are very much targeted at basic research experiments and have to our knowledge not been applied to qPCR assays carried out in the context of clinical trials. This report details the use of the MIQE qPCR app for iPhone (App Store, Apple) to assess the MIQE compliance of one clinical and five pre-clinical trials. This resulted in the need to include 14 modifications that make the guidelines more relevant for the assessment of this special type of application. We also discuss the need for flexibility, since while some parameters increase experimental quality, they also require more reagents and more time, which is not always feasible in a clinical setting.