Most optimized donor-acceptor (D-A) polymer bulk heterojunction (BHJ) solar cells have active layers too thin to absorb greater than ∼80% of incident photons with energies above the polymer's band gap. If the thickness of these devices could be increased without sacrificing internal quantum efficiency, the device power conversion efficiency (PCE) could be significantly enhanced. We examine the device characteristics of BHJ solar cells based on poly(di(2-ethylhexyloxy)benzo[1,2-b:4,5-b′]dithiophene-co-octylthieno[3,4-c]pyrrole-4,6-dione) (PBDTTPD) and [6,6]-phenyl-C61-butyric acid methyl ester (PCBM) with 7.3% PCE and find that bimolecular recombination limits the active layer thickness of these devices. Thermal annealing does not mitigate these bimolecular recombination losses and drastically decreases the PCE of PBDTTPD BHJ solar cells. We characterize the morphology of these BHJs before and after thermal annealing and determine that thermal annealing drastically reduces the concentration of PCBM in the mixed regions, which consist of PCBM dispersed in the amorphous portions of PBDTTPD. Decreasing the concentration of PCBM may reduce the number of percolating electron transport pathways within these mixed regions and create morphological electron traps that enhance charge-carrier recombination and limit device quantum efficiency. These findings suggest that (i) the concentration of PCBM in the mixed regions of polymer BHJs must be above the PCBM percolation threshold in order to attain high solar cell internal quantum efficiency, and (ii) novel processing techniques, which improve polymer hole mobility while maintaining PCBM percolation within the mixed regions, should be developed in order to limit bimolecular recombination losses in optically thick devices and maximize the PCE of polymer BHJ solar cells.