The necessity of validating satellite measurements of atmospheric chemical constituents with supplementary in situ measurements leads to problems with interpretation of the inevitable differences that arise because of measurement resolution or imperfect collocation, especially for highly heterogeneous fields. In this paper the contribution of small-scale structure to measurement differences is estimated from high-resolution aircraft measurements of atmospheric trace gases. The analysis uses the statistics of fractional differences in mixing ratio across a range of scales to estimate the contribution of real variability to differences in noncollocated measurements. The differences depend on the particular chemical tracer, location and season. We find a range of behavior: Differences of 50% across horizontal scales 100 km or less are fairly common for tropospheric water vapor under convective conditions, or carbon monoxide in regions influenced by biomass burning. Ozone varies by about 4--12% in the lower stratosphere and 15--25% in the upper/middle troposphere across scales of about 150 km. The effect of coarse satellite measurement resolution is also estimated by comparing point measurements to locally averaged measurements and is found to reduce the occurrence of large tracer differences. The choice of coincidence lengths should be based on both the scale-dependent variability and a priori estimates of satellite accuracy if real variability is to remain small relative to satellite measurement uncertainties. For satellite instrument uncertainties of about 10%, coincidence lengths for ozone should be less than 50 km in the upper troposphere and less than 100 km in the lower stratosphere.