The objective of this work is to study the uncertainties involved in the modelling of the soil-pile interaction concerning their influence on the prediction of the dynamic structural response of monopile offshore wind turbine support structures. Two main issues are identified and addressed: the adequacy of the method used to deal with the soil-pile interactions and the adequacy of the soil properties reflecting the behaviour of the soil. The present study develops an approach that defines the penetrated pile length depending on the soil profile. Also, a parameter is defined to avoid the excessive usage of steel for the penetrated pile structure. The uncertainties are included in the probabilistic free vibration analysis and the contribution of each random variable to the scatter of the response is estimated by performing a sensitivity analysis. The results indicate that the uncertainty involved in the modelling of the soil profile has a significant effect on the coefficient of variance of the natural frequency, which is a serious issue to be considered in the fatigue life assessment of offshore wind turbine support structures.