An electroless gold deposition method was used to deposit Au nanotubules within the pores of a polycarbonate template membrane. Membranes containing Au nanotubules with inside diameters of 2 and 3 nm were prepared for these studies. Thiols were chemisorbed to the inside tubule walls in order to change the chemical environment within the tubules. The effect of the chemical environment within the tubules on the transport properties of the tubule-containing membrane was investigated. Membranes modified with HS-C(16)H(33) preferentially transported hydrophobic permeant molecules. When a homologous series of permeant molecules was used, the most hydrophobic permeant was preferentially partitioned into and transported by the HS-C(16)H(33) derivatized membrane. In addition, the effect of alkyl chain length (R), in a homologous series of thiols R-SH, was investigated. Hydrophobic permeant molecules were preferentially partitioned into and transported by membranes containing the largest alkyl group. In contrast, membranes modified with HS-C(2)H(4)OH preferentially transported the more hydrophilic permeant pyridine. Finally, we show here that the HS-C(16)H(33) derivatized membrane can be used to separate hydrophobic species from hydrophilic species.