Classical molecular dynamics (MD) simulations of nanoindentation tests are performed in defect-free at 300, 600 and 1000 K and defected crystals at 300 and 600 K of pure Fe and Fe-9Cr alloy. The aim of the work is to evaluate the effect of the presence of various defects specific to neutron/heavy ion irradiation (i.e., voids, dislocation loops and Cr precipitates) on the material response during the early stages of nanoindentation (i.e., at indentation depths up to 20 Å). We establish that even a relatively large density of the radiation defects (∼1024 m−3) does not induce any significant change in the material response, i.e., it is not unambiguously detectable at the force-depth curves neither in pure Fe nor in Fe-9Cr alloys. The macroscopic parameters, which can be derived from these curves, such as hardness and reduced modulus, calculated in the crystals with and without radiation defects also cannot clearly reveal the contribution from the presence of the radiation defects given the resulting uncertainty of their extraction. However, several distinct features typical for nanoindentation tests observed in crystals with radiation defects only were identified, such as a) obstruction of emission of dislocation loops under the indenter during loading for crystals with precipitates and dislocation loops, and b) special residual imprint pattern for crystals with dislocation loops. The results of this work provide useful data for the parameterization and validation of the higher-scale methods, such as dislocation dynamics and (crystal plasticity-) finite-element method. The details of the transferability of MD results to these methods are also discussed.