We present a study on hot electron transport through Au/ molecule/ n-GaAs001 diodes via ballistic electron emission microcopy BEEM. The molecules in the structure form a monolayer of either octanedithiol HS – CH 2 8 –SH or hexadecanethiol HS – CH 2 15 –CH 3 . For the dithiol case, the presence of the molecular interlayer leads to undetectable BEEM transmission. Whereas a small photoinduced collector current is detected at random locations at a forward reverse scanning tunneling microscopy STM tip voltage of −1.43± 0.01 V +1.50± 0.02 V. In comparison, with monothiol diodes, or diodes where the molecules are sandwiched between two Au films Au/ molecule/ Au/ GaAs, the BEEM transmission remains a significant fraction of the reference diode signal 30%–80% with a slight increase in the ballistic transport threshold voltage −1.0 to − 1.1 V from that of the reference Au/ GaAs diodes −0.89 V. Auger depth profiling and cross-sectional transmission electron microscopy show that Au-molecule intermixing occurs in Au/hexadecanethiol/GaAs but not in Au/octanedithiol/GaAs diodes. The suppression of BEEM signal and the detection of STM-induced photocurrent in the Au/octanedithiol/GaAs case are consistent with an insulating monolayer containing pinholes or recombination centers with densities of 1 every 25 25 nm 2 or 2000 m −2 . © 2007 American Institute of Physics.