The natural frequency of soils is one of the important factors in the study of vulnerability to earthquakes. In areas characterized by soft sediments, the maximum amplitude of ground motion is common that lead to enhanced seismic hazard and risk. To map natural frequency of soil in Zanjan, microtremor horizontal-to-vertical spectral ratio (HVSR) method has been conducted. Especially, we used Nakamura’s method on ambient noise records. Ambient noise was recorded in 41 sites in a pre-designed profile. At each site, the noise was recorded for at least one hour long. The results of this study represent there was one amplification peak in most stations. Considering the first peaks, the natural frequency of soil decreases from north to south in the city. The second peak was always more than 3 HZ. The second peak is related to a shallow thin and low-velocity sedimentary layer. To evaluation of results, the data for standard penetration test of boreholes were collected and shear wave velocity was estimated. Using the shear wave velocity obtained from the boreholes, we estimated the thickness of soil from the measured natural frequency of soils employing quarter wavelength law. In general, the results of two methods were significantly near to each other.