Patterned self-assembled monolayers of functionalised alkane thiols were prepared on gold substrates, using UV-photolithography. Two alkane thiols, 11-mercaptoundecanoic acid (MUA) and a fluorinated decane thiol (FDT, CF3(CF2)7CH2CH2SH) were used to fabricate chemically structured surfaces which served as templates for zinc oxide (ZnO) crystallisation. When these patterns, containing high (MUA) and low (FDT) surface energy regions were exposed to a 10 mM zinc nitrate crystallising solution, nucleation occurred selectively on the low energy regions. After 90 min, hexagonal prisms had grown upright on these areas. The crystal growth is uniform with a crystal length of about 1 mum and a diameter between 50 and 100 nm. We attribute the selective growth to a combination of crystallographic frustration of the zinc ions on the high energy regions and an accumulation of hydroxide ions on the low energy regions.