The effects of controlled atmosphere on the metabolism of Golden Delicious and Rome Beauty apples, Anjou pears, and Lambert and Bing cherries were studied with respect to changes caused in the normal metabolic functions carried on during storage of these fruits. Atmospheres consisting of 1.5 per cent CO2 and 2.5 per cent O2 for the apples and pears and 10.5 per cent CO2 and 2.5 per cent O2 for the cherries were employed. Fungi of the strains Botrytis alli, Rhizopus nigricans, and Penicillium expansum were subjected to controlled atmospheres at 21° C to determine the toxic effect of CA. The fungi were grown on agar plates instead of fruit to prevent bias, such as condition of the fruit. Periodically, fruit was taken directly from the storage treatments and analyzed for CO2 evolution, for total and reducing sugars, organic acids, amino acids, and cytochrome c oxidase. Fruits were also taken from the storage treatments and held for a specific time at 15° C before analysis. The CA used in this experiment had an inhibitory effect on the fungi that were used. Botrytis alli and Penicillium expansum were particularly susceptible. It was found the height of the mycelial mat was less, the mycelium growth was less, and while sporulation was not eliminated, it was severely retarded. Combinations of CA and lowered temperatures should attain a high degree of fungal control. The results showed that CA had an inhibitory effect on the metabolic system of stored fruits. The specific areas of metabolic inhibition are not known exactly. This inhibition does not appear to be of a permanent nature as shown by the post storage analysis. Any differences that occurred in the CA stored fruit as contrasted to the fruit from the conventional stored fruit appeared to be able to correct themselves once they were removed from the CA.