The successful application of the grafting technique depends on the identification of stress and pathogen-resistant rootstock (RS), and on the compatibility of the grafted union in terms of fast formation of the vascular connections between the rootstock and the scion and rapid resumption of root and shoot growth. A series of studies, using compatible and incompatible Cucurbita rootstocks, grafted with melon (Cucumis melo L.) scion ('Arava'), were conducted in order to identify metabolic and physiological factors which may be associated with the level of grafting compatibility. In order to increase the differential compatibilities, the grafted seedlings were exposed to either control (22/28 degrees C) or high (28/35 degrees C) temperature conditions starting at 7 days after grafting. Grafting compatibility was dependent on temperature conditions. Twenty days from grafting the rootstock part collapsed only in the non-compatible grafted seedlings under high temperatures but not under normal temperatures. Water uptake and sugar distribution between plant canopy and root measured 14 days under these conditions, and before incompatible transplants collapsed, were not correlated with the differential compatibility. At that stage histo-chemical staining showed that reactive oxygen species (ROS) generation was enhanced under high temperatures in the grafting zone in both compatible and incompatible graft combinations. In this paper we describe a mechanism which may be responsible for grafting incompatibility between Cucurbita RS and melon scion. We suggest that upon formation of the RS-scion continuum, the hormonal balance, especially of auxin and ethylene, required for proper root development, is impaired in incompatible grafting union. This impairment is initiated by the auxin, transported from the scion to the root, which in incompatible RS, triggers ethylene production, ROS generation and root growth inhibition and degeneration. In compatible RS, a variety of mechanisms may operate to either reduce auxin activity in the RS and/or reduce ROS production and activity.