Abstract: A continuous CO2 measurement system was developed to monitor the CO2 exchange rate of the whole canopy of grafted transplants using semi-open multiple chambers. Air heating or cooling and humidification inside a healing box were under control, if needed. To test the system, the gas exchange rate of the cucumber (Cucumis sativus L.) transplants grafted onto pumpkin (Cucurbita maxima cv. ‘New-Shintozwa’) was analysed. During the healing and acclimatisation of the grafted cucumber plants, the air temperature in the box remained constant at night but ranged above 1°C of a set value under high humidity in daytime. The relative humidity was kept within the set point during the daytime, and it nearly reached 100% at night when not controlled. The cucumber seedlings were exposed to different water stresses before grafting, and the water potentials of each treatment were −0.579 (non-stressed), −0.814 (mildly water-stressed), and −0.870MPa (strongly water-stressed) on grafting. At the water-stressed scions, leaf expansion was inhibited by 30.9–53.3% compared with the non-stressed scions. Therefore, the gas exchange rates of the strongly water-stressed scions based on the leaf area were decreased to 72.7% compared with the non-stressed scions. After grafting, the apparent photosynthesis of the transplants of all treatments was negative, with higher respiration in the strongly water-stressed scions during the initial period of healing. However, they turned to positive values and exceeded those of the non-stressed scions from three days after grafting. This result provides critical information that the water column is physiologically connected between the stock and scion within two days after grafting. As a result of water stress, the leaf area and dry weight of the transplants in the strongly water-stressed scions were inhibited by 67.5% and 83% compared with the non-stressed scions at the end of acclimatisation. In contrast, the relative growth rate and graft-take of the strongly water-stressed transplants were slightly increased, which suggests that the water stress prior to grafting alleviated the water demand of the scion. This system may provide useful information for diagnosis at the early stage by monitoring the whole canopy''s photosynthesis over a long term. [Copyright &y& Elsevier]