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Soil compaction heterogeneity and water content are supposed to be decisive factors influencing plant growth. Our experiment focused on simulation of two soil moisture levels (0.16 and 0.19 g/g) plus two levels of clod proportion (30 and 60% volume) and their effects on root and leaf variables of maize (Zea mays L.). We studied number of primary and lateral roots as well as primary root length at the particular soil depths. Statistical tests showed that the decrease rate of the number of roots versus depth was significantly affected by the two studied factors (P < 0.01). Soil moisture and clod occurrence, interactively, affected leaf biomass (P = 0.02). Presence of clods modified root morphological features. Particularly, the diameter of primary roots in the clods was significantly higher than of those grown in fine soil (P < 0.01). For primary roots, which penetrated clods, branching density decreased considerably for the root segments located just after the clods (P = 0.01). Regarding their avoidance to clods and tortuosity, large differences were found between primary roots grown in the contrasting soil environments.