The influence of the microstructure of poly(3-hexylthiophene) (P3HT) on its photodegradation upon exposure to UV-visible light was studied. High-regioregular (>98%) and low-regioregular (<95%) P3HTs with different molecular weights, dispersities and purities were submitted to irradiation under accelerated artificial ageing conditions. While the molecular weight had no effect on the photodegradation rate, a linear relationship was observed between the photodegradation rate and the regioregularity. The higher photo-instability of low-regioregular P3HTs, which have low crystalline phase content, could be due to the fact that the radical chain oxidation occurs predominantly in the amorphous phase of the polymer. Low-regioregular P3HTs also have a higher number of impurities, especially Fe residues, which are well known for their photocatalytic effect. The results also show that, at low concentrations, oxidation products are able to quench the singlet state of P3HT by acting as electron traps, and that the shortest wavelengths of solar light are the most harmful. Finally, the photooxidation of P3HT leads to the formation of low-molecular-weight carboxylic acids that can easily diffuse and migrate out of low-regioregular P3HT thin films. These results are therefore relevant to the preparation, storage and lifetimes of P3HT-based organic solar cells.