Polar mesoscale cyclones over the subarctic are thought to be an important component of the coupled atmosphere–ocean climate system. However, the relatively small scale of these features presents some concern as to their representation in the meteorological reanalysis datasets that are commonly used to drive ocean models. Here polar mesocyclones are detected in the 40-Year European Centre for Medium-Range Weather Forecasts (ECMWF) Re-Analysis dataset (ERA-40) in mean sea level pressure and 500-hPa geopotential height, using an automated cyclone detection algorithm. The results are compared to polar mesocyclones detected in satellite imagery over the northeast Atlantic, for the period October 1993–September 1995. Similar trends in monthly cyclone numbers and a similar spatial distribution are found. However, there is a bias in the size of cyclones detected in the reanalysis. Up to 80% of cyclones larger than 500 km are detected in MSL pressure, but this hit rate decreases, approximately linearly, to ∼40% for 250-km-scale cyclones and to ∼20% for 100-km-scale cyclones. Consequently a substantial component of the associated air–sea fluxes may be missing from the reanalysis, presenting a serious shortcoming when using such reanalysis data for ocean modeling simulations. Eight maxima in cyclone density are apparent in the mean sea level pressure, clustered around synoptic observing stations in the northeast Atlantic. They are likely spurious, and a result of unidentified shortcomings in the ERA-40 data assimilation procedure.