An evaluation of the effects of soil structural heterogeneity on maize (Zea mays L.) root system architecture was carried out on plants grown in boxes containing fine soil and clods. The clods were prepared at two levels of moisture (0.17 and 0.20 g/g) and bulk density (ranges 1.45–1.61 g/ml and 1.63–1.79 g/ml). Soil moisture directly affected the probability of clod penetration by maize roots. Primary roots inside the clods manifested morphological deformations in the form of bends. We observed a significant increase of bends per root length at lower soil moisture (P = 0.02). Root diameter and branching density increased, and lateral root length decreased considerably inside the clods. However, once emerging out of the clods and into free soil, values of all three characteristics remained low. While changes in root diameter were caused mainly by clod moisture (P < 0.05), length of lateral roots was related to bulk density (P < 0.01). Branching density was modified exclusively by an interactive effect of both factors (P < 0.05)