We studied the effects of hyperhydricity on subcellular ultrastructure and physiology of leaves during in vitro regeneration of apple plants. Morphological, anatomical and ultrastructural differences between healthy leaf tissues obtained from greenhouse-grown plants and healthy and hyperhydric leaves obtained from shoots raised from nodal shoot explants in a bioreactor were investigated by electron microscopy and confocal laser scanning microscopy. Compared with healthy leaves, hyperhydric leaves showed abnormal, often discontinuous development of the epidermis and cuticle. Stomata were malformed. The leaf lamina appeared thickened and was characterized by poor differentiation between the palisade and spongy mesophyll tissue. Hyperhydric leaves had a significantly lower chloroplast number per cell and chloroplasts showed reduced thylakoid stacking compared with healthy leaves. Hyperhydricity resulted in a general decrease in concentrations of reduced and oxidized pyridine nucleotides, reflecting a reduction in metabolic activity. The activities of antioxidant enzymes, such as superoxide dismutase, catalase, ascorbate peroxidase and glutathione reductase were higher in hyperhydric leaves than in healthy leaves, indicating that hyperhydricity was associated with oxidative stress. Chlorophyll fluorescence measurements provided evidence of oxidative damage to the photosynthetic machinery in hyperhydric leaves: photochemical efficiency of photosystem II, effective quantum efficiency and photochemical quenching were all lower in hyperhydric leaves compared with healthy leaves.