Frequency-domain approach for fatigue damage estimation and lifetime prediction of mechanical components is often used for its computational efficiency and the capability to give a synthetic representation of a random process. The problem with the approach is that the input data, the stress power spectral density (PSD), may not include the information about potential small amount of high amplitude cycles which can substantially increase the accumulated fatigue damage. The paper investigates the scatter of the accumulated damage in generated random stress histories and compares them to the results obtained by a frequency-domain approach—the Dirlik method. The results show a possibility of a severe underestimation of accumulated damage when using frequency-domain approach. In case a typical stress, history of a certain mechanical component includes sporadic high amplitude cycles their effect shoud be taken into consideration when using frequency-domain approach.