The host-pathogen combinations - Malus domestica (apple)/ ‘Candidatus Phytoplasma mali´, Prunus persica (peach)/‘Ca. P. prunorum´ and Pyrus communis (pear)/‘Ca. P. pyri´ show different courses of diseases although the phytoplasma strains belong to the same 16SrX group. While infected apple trees can survive for decades, peach and pear trees die within some weeks or years. To this date, neither morphological nor physiological differences caused by phytoplasmas have been studied in these host plants. In this study, phytoplasma-induced morphological changes of the vascular system as well as physiological changes of the phloem sap and leaf phytohormones were analysed and compared with non-infected plants. Unlike peach and pear, infected apple trees showed substantial reductions in leaf and vascular morphology, affecting phloem mass flow. In contrast, in pear mass flow and physicochemical characteristics of phloem sap increased. No changes in phytohormone levels were detected in pear but in apple and peach trees, where defence- and stress-related phytohormones increased. Compared with peach and pear trees, data from apple suggest that the long-lasting morphological adaptations in the vascular system, which likely cause reduced sap flow, triggers the ability of apple trees to survive phytoplasma infection. Some phytohormone-mediated defences might support the tolerance.