This paper proposes a new non-parametric method to estimate the power spectral density of atmospheric radar signals using uniform filter banks through polyphase approach. The performance of proposed method is investigated for a simulated broadband and narrowband signals. This method reduces the variance without affecting the resolution and improves the signal to noise ratio significantly when compared to the existing method (periodogram/modified periodogram). The variance reduction is observed to be more in case of narrowband signals. The method has the computational cost similar to modified periodogram approach. This method is tested for practical atmospheric data collected at NARL, Gadanki, India, through the mesosphere-stratosphere- troposphere (MST) radar, back scattered echoes, in particular from high altitudes, which has low signal to noise ratio. Results have been validated using simultaneous Global Positioning System (GPS) Sonde data. © 2009 Elsevier Inc. All rights reserved.