Surface-enhanced Raman scattering (SERS) of adsorbed molecules on gold nanorods (NRs) with dimensions of 10 nm x 27 nm was studied on silica surface with low to high surface coverage of NRs. The study was carried out to investigate both the dependence of the SERS intensity on the number of NRs and the NRs spacing on the silica surface. SERS of adsorbed molecules such as 2-aminothiophenol (2-ATP) and the capping molecules (hexadecyltrimethylammonium bromide) was studied on these surfaces using a near-IR laser excitation source (1064 nm). To produce silica surfaces covered with NRs, two approaches were used. In the first approach, monodispersed NRs gradually deposited from solution to silica surface and their number was increased by increasing the deposition time. In the second one, the NRs were first aggregated in solution and then deposited on the surface. Although using the first approach it was possible to prepare surfaces with high NR surface coverage, SERS intensity was found to be stronger for adsorbed molecules on surfaces covered with aggregated NRs. The observed increase in the SERS intensity in the case of aggregation was attributed to the enhancement of the electric field between the particles in the aggregates. It is shown that aggregated NRs in comparison with aggregated nanospheres (NSs) have stronger SERS enhancement under similar experimental conditions. In this comparison, some of the enhanced vibrational bands of 2-ATP on aggregated NRs are weakly enhanced or absent on aggregated NSs. Monitoring the SERS intensity of adsorbed 2-ATP versus its exposure time to the aggregated NRs shows that the SERS intensity of the adsorbed molecules reaches saturation, whereas the peak intensities of the capping molecules remain unchanged. The intensity saturation was discussed in terms of factors such as the saturation of the SERS active sites for 2-ATP on the gold surface and the partial damping of the plasmon band due to the stronger interaction of the adsorbate molecules with the metal surface.