Poly(3-hexylthiophene) (P3HT) films and P3HT / fullerene photovoltaic cells have been p-doped with very low levels (< 1 wt. %) of molybdenum tris[1-(trifluoromethylcarbonyl)- 2-(trifluoromethyl)-ethane-1,2-dithiolene]. The dopants are inhomogenously distributed within doped P3HT films, both laterally and as a function of depth, and appear to aggregate in some instances. Doping also results in subtle changes in the local and long range order of the P3HT film. These effects likely contribute to the complexity of the observed evolutions in conductivity, mobility and work function with doping levels. They also negatively affect the open-circuit voltage and fill factor of solar cells in unexpected ways, indicating that dopant aggregation and non-uniform distribution can harm device performance.