We have investigated electrical properties of symmetric alkanethiolate bilayer junctions formed by contacting two hanging mercury drop electrodes each coated initially with a single alkanethiolate monolayer. Using potentiodynamic, current transient and ac impedance methods, we have shown that the initial, largely all-trans structure of the bilayers becomes disordered with time as a result of the van der Waals and coulombic forces squeezing the junction. Chain disorder involves both gauche defects and chain intercalation at the mid plane of the bilayer. We showed that the latter progress more rapidly for junctions formed with longer alkanethiols. To characterize the strength of the electronic coupling across these junctions, we measured the decay constant beta for the native bilayers featuring largely all-trans conformation and for the disordered junctions. The former was obtained from fast scan (50-500 V s(-1)) j-V experiments and yielded beta = 1.29 per CH2 group (corresponding to beta = 1.0 Angstrom (-1)). Impedance measurements were used to investigate properties of the disordered junctions. Electron tunneling resistance and junction capacitance were measured simultaneously. The plot of the logarithm of junction resistance measured at zero voltage bias versus thickness gave beta = 1.6 Angstrom (-1) These measurements demonstrate that the efficiency of electron tunneling decreases substantially when alkanethiolate chains become disordered.