The conjugated polymer poly(3-hexylselenophene-2,5-diyl) (P3HS) is a promising donor material for organic solar cells as its absorption covers a large part of the visible spectrum up to 730 nm. We investigate bulk heterojunctions of P3HS and the fullerene derivative [6,6]-phenyl C61-butyric acid methyl ester as the active layer in organic photovoltaic devices. Annealing of the respective samples leads to the formation of needle-like structures that we identify as P3HS whiskers by means of low-energy scanning transmission electron microscopy using a high-angle annular dark-field detector. A quantitative description of the size of the nanostructures was elaborated by means of spatial Fourier analyses. The results of electron microscopic studies are correlated with the macroscopic optoelectronic device properties, that is, solar cell performance parameters, with changes in the absorption spectrum and with the impact on the time-dependent device photoresponse. (C) 2011 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys, 50: 198-206, 2012