Fresh-cut produce continues to be a rapidly growing industry. However, there is little information available on storage conditions for many commodities, particularly for fresh-cut tomato slices. A major problem with fresh-cut tomato slices is their short shelf-life. The best method to extend shelf-life is refrigerated storage, preferably around 4 to 5 °C. Unfortunately, tomato tissue is susceptible to chilling injury at such temperatures. Experiments were conducted to compare changes in quality of slices from red tomato (Lycopersicon esculentum Mill.) fruit during storage at 5 or 10 °C under various modified-atmosphere conditions. In this study, we used the fourth uniform slice from the stem end and analyzed for various quality attributes during the storage period. At both 5 and 10 °C storage temperatures, ethylene concentration in containers sealed with Film A (oxygen transmission rate of 60.3 or 77.9 ml per hour per m2 at 1 atm and 99% relative humidity at 5 or 10 °C, respectively) was higher than that sealed with Film B (oxygen transmission rate of 87.4 or 119.4 ml per hour per m2 at 1 atm and 99% relative humidity at 5 or 10 °C, respectively), during storage. In addition, chilling injury, as measured by percent of slices showing some water soaked-areas, in containers sealed with Film B was higher than that of slices in containers sealed with Film A. The percent of visible fungal growth of slices was roughly correlated with the degree of chilling injury, as measured by the percent of slices showing some water soaked-areas. After 13 days of storage at 5 °C, slices stored in containers with a beginning atmospheric composition of 12% CO2 /1% O2 were firmer, compared to slices given the other treatments. After 9 days of storage at 10 °C, no visible fungal growth was observed on slices in containers with a beginning atmospheric composition of 12% CO2/1% O2 or 12% CO2/20% O2. However, slices in containers with a beginning atmospheric composition of air, or 4% CO2/1 or 20% O2 and 8% CO2/1 or 20% O2 did show visible signs of fungal growth at 25%, 33%, 46%, 29%, and 100% of infected slices, respectively. Slices in containers given all treatments, with the exception of 12% CO2/1% O2, had visible fungal growth after 15 days of storage at 5 °C. Slices in containers containing eight slices had less chilling injury and visible fungal growth than those containing four slices. Chilling injury of slices stored in completely enclosed plastic containers, similar to those commonly observed in grocery food stores, was over 7-fold higher than chilling injury observed in slices containers covered with Film A after 12 days of storage at 5 °C. However, there were no significant differences in the amounts of the volatiles we measured, i.e., ethanol, ethyl acetate, hexanol and hexanal, between the two container types. These results suggested that modified-atmosphere packaging storage can extend shelflife, as well as inhibit chilling injury in fresh-cut tomato slices.