Site effects may be assessed using a standard soil classification parameter, VS30 (the harmonic average shear‐wave velocity in the first 30 m); however, this index does not account for the complexity of the velocity profile, especially its variability at depth. In the present study, in addition to VS30, we propose consideration of the gradient of the VS profile from 0 to 30 m depth, denoted B30. A lower gradient value means low velocity increases with depth; a higher gradient indicates a rapid velocity increase with depth in the shallow layers. In addition, we consider the fundamental resonance frequency of the soil (f0), which has been shown to be a relevant parameter for site‐effect assessment and which is obtained from the empirical site response. Using the Japanese KiK‐net database, we analyze the variability of the VS profiles and the empirical borehole site responses of selected sites through the VS30, the velocity gradient B30, and f0. We select 289 sites for which the 1D linear numerical modeling is close to the empirical site response and a VS at the downhole station is greater than 1000 m/s. For a given VS30 class, B30, and f0 can be used to distinguish between two types of sites: deep sedimentary sites and sites with high velocity contrast at shallow depths. We find that, even if the gradient is calculated using shallow information, its use improves the site amplification characterization, compared to using only VS30, by reducing the intersite site‐response variability. As expected, however, this improvement is limited for deep sedimentary sites. On the other hand, f0 is able to reduce the intersite response variability for deep sedimentary sites even though it is limited to specific VS30 classes. Thus, the combined use of VS30, B30, and f0 improves the assessment of linear site amplification.