Magnetic reconnection is the most significant process that results in the transport of magnetized plasma into and out of the Earth's magnetosphere-ionosphere system. There is also compelling observational evidence that it plays a major role in the dynamics of the solar corona, and it may also be important for understanding cosmic rays, accretion disks, magnetic dynamos, and star formation. The Earth's magnetosphere and ionosphere are presently the most accessible natural plasma environments where magnetic reconnection and its consequences can be measured, either in situ or by remote sensing. This paper presents a complete methodology for the remote sensing of magnetic reconnection in the magnetosphere from the ionosphere. This method combines measurements of ionospheric plasma convection and the ionospheric footprint of the reconnection separatrix. Techniques for measuring both the ionospheric plasma flow and the location and motion of the reconnection separatrix are reviewed, and the associated assumptions and uncertainties are assessed, using new analyses where required. Application of the overall methodology is demonstrated by the study of a 2-h interval from 26 December 2000 using a wide range of spacecraft and ground-based measurements of the Northern Hemisphere ionosphere. This example illustrates how spatial and temporal variations in the reconnection rate, as well as changes in the balance of magnetopause (dayside) and magnetotail (nightside) reconnection, can be routinely monitored, affording new opportunities for understanding the universal reconnection process and its influence on all aspects of space weather.