Indirect determination of meridional winds using ground-based ionosonde data from low latitude regions, under the assumption that the thermosphere and the F-region of the ionosphere behave as a closely coupled system, has been critically examined. The significance of neutral temperature and its variations in the above estimates has been demonstrated through individual case studies after duly validating the procedure adopted. Since the measured neutral temperatures have shown large deviations from the existing atmospheric models on many occasions and more so during high solar activity periods, it has been shown that the neutral temperature effects on the F-region heights should be properly accounted for before one attempts to estimate meridional winds. However, it has also been shown that during low solar activity periods, use of atmospheric models may still provide a fairly reasonable average picture. Examples of these effects are presented and discussed.