Many studies have investigated the effect of elevated CO2 (eCO2) in wheat, although few have evaluated the potential of genotypic variability in the response. Such studies are the next logical step in wheat climate change adaptation research, and they will require the evaluation of large numbers of genotypes. For practical reasons the preliminary studies are most likely to be conducted in controlled environments. There have been concerns that the root restriction related to container-grown plants can influence (1) the response to eCO2, (2) the detection of genotypic variability for various traits of interest, and (3) the ability to find the genotypes most responsive to eCO2. In the present study we evaluated two sizes of container - 1.4L pots and 7.5L columns - side-by side in a glasshouse environment and found that for 14 of 23 traits observed environment effects (ambient CO2, eCO2 or eCO2 and high temperature) were not consistent between plants grown in pots and in columns. More importantly, of the 21 traits showing genotypic variability, only 8 showed consistent genotype differences and rankings across both container types. Statistical analyses conducted separately for plants grown in pots or in columns showed different cultivars as being the most responsive to elevated CO2 and would thus, have led to different conclusions. This study is intended as a message of caution to controlled environment experimenters: using small containers can artificially create conditions that could either hide or overly express genotypic variability in some traits in response to eCO2 compared with what might be expected in larger containers.