Numerous fields of computational Earth system research require a precise account of variations in the relative atmospheric angular momentum (AAM). Since zonal winds from reanalysis data sets of ERA-40 (ECMWF) and NCEP1 (NCEP/NCAR) are frequently used to compute relative AAM estimates it is critically important to understand uncertainties in these data products. Here, we discuss the varying degree of structural and internal uncertainties associated with ERA-40 and NCEP1 zonal wind data in the tropical Pacific troposphere and lower stratosphere. We assess these uncertainties by quantifying differences in relative AAM computed from reanalyses wind data (1958–2000), that are subsequently compared to a 10-year record of radiosonde observations carried out in the tropical Pacific where reanalyses data differ most. While our analysis suggests that in general differences between reanalysis data and observed tropical winds in the Pacific are not significantly different from each other, we found varying degrees of discrepancies at each radiosonde site. Zonal winds in NCEP1 data (RMS = 1.84 ms−1) reproduce less bias in tropospheric easterly winds than ERA-40 (RMS = 3 ms−1), while for the lower stratosphere ERA-40 data fit better westerly winds (RMS = 3.95 ms−1) than NCEP1 (RMS = 5.03 ms−1). Anomalies in zonal tropical wind fields can be induced by large mountain and friction torques that efficiently affect Earth's rotation rate. Hence, a precise account of the wind term in reanalysis data directly determines the accuracy of computed estimates of relative AAM.