In a three-year study, the effect of two winter pruning treatments (strong and weak) on apple scab (Venturia inaequalis) and powdery mildew (Podosphaera leucotricha) was evaluated on six apple cultivars (`Rewena', `Elstar', 'Liberty', 'Gala', 'Pilot' and `Jonica') in two environmentally-benign apple production systems (integrated and organic). Results on apple scab showed that compared to the integrated production system, the pathogen caused significantly more infection on the leaves of cvs. `Elstar', 'Gala' and `Jonica' in the organic production system. The effect of pruning treatments on apple scab was mainly detectable on the cultivars susceptible to the disease such as cvs. 'Gala' and `Jonica'. The weak pruning correlated with a higher level of apple scab infection than the strong pruning, especially in the organic production system. Primary mildew infection was very low in both protection systems (below 2 %), therefore, effect of pruning on primary mildew infection could not be analysed. Low secondary mildew incidence was detected in the organically treated orchard part; however, incidence of powdery mildew was significantly higher (P> 0.05) on cvs. 'Elstar', 'Pilot' and `Jonica' in the integrated orchard part compared to cvs. 'Gala', 'Rewena' and 'Liberty'. The highest incidence of mildew was on cv. 'Elstar'. Pruning had very low effect on incidence of secondary mildew infection on leaves.