Abstract In experimental structural dynamics, reliable estimation of Frequency Response Functions (FRF) is important to correctly characterize a mechanical system. In Experimental Modal Analysis (EMA), the FRFs are used as input to a modal parameter estimation algorithm to obtain the modal characteristics of the system. Errors due to noisy measurements are inevitably present in the FRFs and propagate to the modal parameters. A consistent FRF-estimator with low uncertainty is therefore needed. Different FRF estimators have been proposed with some consistency when certain noise-related assumptions are fulfilled (H1, H2, etc.). To choose the appropriate frequency response function estimator, information about the noise in the experimental setup is desirable. In this work it is shown how to use measurements of noise, to characterize different noise components in the experimental setup and determine the appropriate number of averages needed for the experimental setup. The identified noise components can be used to identify the main source of uncertainty in the experimental setup and which FRF estimator to use.