The fabrication of organic electronics devices onto flexible polymer substrates by roll-to-roll (r2r) processes requires the use of in-line quality control tools for the optimization of the optical and electronic properties of semiconducting, electrodes and barrier layers and their thickness that will achieve the required performance and lifetime of the devices. This paper focuses of the investigation of the optical properties of r2r printed nanolayers for organic photovoltaics, by in-line spectroscopic ellipsometry (SE) in the visible-far ultraviolet spectral region. This is performed by a prototype very fast stand-alone SE unit adapted onto a lab-scale r2r system. First, we test the stability and precision of measurements to validate the optical measurements and the analysis procedure. Afterward, we report on the robust determination of the thickness and optical properties of barrier thin layers (a combination of SiOx and hybrid polymer bilayers), PEDOT:PSS transparent electrodes and polymer:fullerene (P3HT:PCBM) blends that were gravure printed onto flexible PET substrates in the form of rolls. Finally, we discuss on the effect of the experimental parameters on the optical properties and the quality of the printed nanolayers as determined by the modeling approaches of the in-line measurements. (C) 2013 Elsevier B.V. All rights reserved.