Nitrous oxide (N2O) and methane (CH4) were measured in the upper troposphere and lower stratosphere by multiple instruments aboard the NASA ER-2 aircraft during the 1995--1996 Stratospheric Tracers of Atmospheric Transport (STRAT) and 1997 Photochemistry of Ozone Loss in the Arctic Region in Summer (POLARIS) campaigns. Differences between coincidental, in situ measurements are examined to evaluate the agreement and variability in the agreement between these instruments during each flight. Mean N2O measurement differences for each flight were much smaller than limits calculated from quoted values of N2O measurement accuracy and for all but two flights were ≤8.7 ppb (3.5%). Mean CH4 measurement differences for flights were similarly much smaller than calculated limits and for all but three flights were ≤65 ppb (4.4%). Typical agreement between instruments during flights averaged 6.2 ppb (2.5%) for N2O and 43 ppb (2.9%) for CH4. In contrast, for about half of the flights, the variability of N2O and CH4 measurement differences exceeded limits calculated from quoted values of measurement precision. The typical measurement difference variability (1&sgr;) during a flight averaged ¿8.0 ppb (3.2%) for N2O and ¿43 ppb (2.9%) for CH4. For some flights, large differences or variations in differences are attributable to the poor measurement accuracy or precision of one instrument. It is demonstrated that small offsets between the computer clocks of these instruments can result in significant differences between their coincidental N2O and CH4 data, especially when there is high spatial variability in tracer abundance along a flight track. ¿ 2000 American Geophysical Union