We show that self-assembled vertically aligned gold nanorod (VA-GNRs) superlattices can serve as probes or substrates for ultra-high sensitive detection of various molecules. D-glucose and 2, 4, 6-trinitrotoluene (TNT) have been chosen as model systems due to their very low Raman cross-sections (5.6 × 10-30 cm2·molecule-1·sr-1 for D-glucose and 4.9 × 10-31 cm2·molecule-1·sr-1 for TNT) to show that the VA-GNR superlattice assembly offers as low as yoctomole sensitivity. Our experiment on mixed samples of bovine serum albumin (BSA) and D-glucose solutions demonstrate sensitivity for the latter, and the possible extension to real samples. Self-assembled superlattices of VA-GNRs were achieved on a silicon wafer by depositing a drop of solvent containing the GNRs and subsequent solvent evaporation in ambient conditions. An additional advantage of the VA-GNR monolayers is their extremely high reproducible morphology accompanied by ultrahigh sensitivity which will be useful in many fields where a very small amount of analyte is available. Moreover the assembly can be reused a number of times after removing the already present molecules. The method of obtaining VA-GNRs is simple, inexpensive and reproducible. With the help of simulations of monolayers and multilayers it has been shown that superlattices can achieve better sensitivity than monolayer assembly of VA-GNRs.