Permeation of various gases through elastomeric O-ring seals can have important effects on the integrity of atmospheric air samples collected in flasks and measured some time later. Depending on the materials and geometry of flasks and valves and on partial pressure differences between sample and surrounding air, the concentrations of different components of air can be significantly altered during storage. The influence of permeation is discussed for O2/N2, Ar/N2, CO2, δ13C in CO2, and water vapor. Results of sample storage tests for various flask and valve types and different storage conditions are presented and are compared with theoretical calculations. Effects of permeation can be reduced by maintaining short storage times and small partial pressure differences and by using a new valve design that buffers exchange of gases with surrounding air or by using less permeable materials (such as Kel-F) as sealing material. General awareness of possible permeation effects helps to achieve more reliable measurements of atmospheric composition with flask sampling techniques.