T-shaped bolaamphiphiles composed of a biphenyl rigid core, a semiperfluorinated lateral chain, two polar 1,2-diol groups in the terminal positions and flexible alkyl spacers connecting the polar groups with the biphenyl core have been synthesized and investigated by polarizing microscopy, DSC and X-ray scattering. The influence of spacer length and position of the spacer on the self-assembly in liquid-crystalline phases was studied. A series of four different columnar phases (Col(hex)/p6mm, Col(rec)/p2gg, Col(squ)/p4gm and Col(squ)/p4mm), representing liquid-crystalline honeycomb structures composed of cylinders having hexagonal, pentagonal, and square cross section, were found on increasing the spacer length. It is also shown that introduction of aliphatic spacers in the backbone of the T-shaped bolaamphiphiles replaces the Col(rec)/c2mm phase made up of rhombic cylinders with the Col(squ)/p4mm phase composed of square cylinders. It also causes the 2d lattice of pentagonal cylinders to increase the symmetry from Col(rec)/p2gg to Col(squ)/p4gm. A temperature-dependent second-order phase transition between these two pentagonal cylinder structures was observed for the first time. Beside these effects on cylinder shape and phase symmetry the flexible spacer units also lead to reduced phase transition temperatures and allow adjustment of cylinder side length to envelop a wider range of side-chain sizes. Electron density maps suggest that this may involve sacrificing some of the hydrogen bonds.