Accurate site characterization plays a critical role in the seismic design of structures, and the shear wave velocity (VS) profile of the site is one of the most important parameters in seismic site characterization. VS,30 (the time-averaged VS of the top 30 m soil column), is commonly used for site characterization and site classification in seismic design codes. Based on the site classification, different design response spectra are provided in the codes. However, VS,30 used in the codes does not consider the effect of layering within the soil profile at a given site. Two or more sites with the same VS,30 may have different soil layering configurations, which can result in different amplification factors. The present study focuses on investigating the effect of layering within a soil profile on site amplification factors. Different synthetic soil Vs profiles with the same VS,30 are considered, and 1D equivalent linear ground response analyses are carried out, taking three different input motions, namely Chichi, Kobe, and Bhuj earthquake motions. The reason for choosing three different motions for the analyses is to account for a broader range of seismic scenarios, and thus make the analyses more comprehensive and widely applicable. The different synthetic soil profiles with varying layering configurations used in the study are randomly generated using MATLAB. Equivalent linear method used in the study is the most widely adopted ground response analysis technique by the earthquake engineering community. It offers a time-efficient approach while accounting for soil nonlinearity by utilizing a shear modulus that aligns with the shear strain experienced by each soil layer during cyclic loading and unloading behavior. This ensures consistency in capturing the dynamic response of the soil. All the analyses have been carried out using DEEPSOIL software. The DEEPSOIL software simulates seismic wave propagation through the layered soil profiles while considering the interaction between the soil layers and the incident waves. The study aims to identify and quantify the differences in the amplification factor for different soil profiles having the same VS,30. The results of the study clearly indicate the importance of considering the effect of layering on site amplification and the need to account for the layering effects on the amplification factors given in the codes.