A series of well-defined perfluoroalkyl end-functionalized poly(3-hexylthiophenes) (P3HT) were synthesized by Stifle coupling of stannylated 2-perfluoralkylthiophene with the bromine end of P3HT. The length of the perfluoroalkyl end group was varied from -C4F13 to -C8F17. These polymers were fully characterized and tested in bulk heterojunction solar cells with phenyl-C-61-butyric acid methyl ester (PCBM) as the acceptor. Performance of the solar cells was highest for the unmodified P3HT and decreased as the length of the perfluoroalkyl end increased. The most affected device parameters were the short-circuit current density (J(sc)) and series resistance, pointing to lower charge carrier mobility and poor morphology as the cause for the lower performance. While the morphology of blends did not significantly change with perfluoroalkyl end modification, analysis of blended films by energy-filtered transmission electron microscopy (EF-TEM) revealed wider P3HT domains, consistent with the perfluorinated end groups segregating to the edge or exterior of P3HT domains, causing two domains to join. This study demonstrates that the perfluoroalkyl end group can be detrimental to polymer solar cell device performance, and further work toward understanding the interface between the donor and acceptor phases is required to fully understand this effect.