We have investigated structural distance metrics for linear genetic programs. Causal connections between changes of the genotype and changes of the phenotype form a necessary condition for analyzing structural differences between genetic programs and for the two objectives of this paper: (i) Distance information between individuals is used to control structural diversity of population individuals actively by a two-level tournament selection. (ii) Variation distance is controlled on the effective code for different genetic operators - including a mutation operator that works closely with the applied distance metric. Numerous experiments have been performed for three benchmark problems.