In this work, we applied low-impact energy secondary ion mass spectrometry (known as Sc-Ultra SIMS) and high lateral resolution (NanoSIMS50) to characterize the P3HT/PCBM (poly(3-hexylthiophene)/phenyl C61-butyric acid methyl ester bulk heterojunction photovoltaic (PV) devices. Here we report results obtained on Al/P3HT:PCBM/PEDOT:PSS/ITO (poly(3-hexylthiophene:phenyl C61-butyric acid methyl ester/poly(ethylene-dioxythiophene):poly(styrene sulfonate)/indium tin oxide) using advanced SIMS measurements to monitor 3D molecular compositions and metal/organic interface. The measurements have been performed on as-deposited as well as-annealed samples of Al/polymer interface. Blend macrophase separation and polymer/fullerene distribution have been investigated. Copyright © 2010 John Wiley & Sons, Ltd.