Stump-roots and leaves from different residues of short rotation coppice (SRC) of poplar clones were transformed with microwave assisted pyrolysis to produce bio-oils. These products were obtained with high yield (up to 32.0%) and small water percentage (up to 17.5%), showed low density and viscosity and were fluid at room temperature. Bio-oils were characterized with several analytical techniques: 1 H NMR, IR-ATR, and an original and a quantitative GC-MS method. Acetic and formic acids, acetic anhydride, furanes and various phenols were identified and quantified; among bio-oils a sample with high acetic acid concentration (543.3 mg/mL) was obtained. These techniques let to make possible a detailed study on the bio-oils to define a correlation between their chemical and rheological properties with the clones employed and parameters of the process.