In order to evaluate the performance of different methods for estimation of the vertical eddy diffusivity in thermally stratified lakes, two field studies were conducted in Lake Biwa, Japan and Lake Kinneret, Israel. Lake Biwa experienced three typhoons during the campaign while Lake Kinneret experienced high winds in the afternoons. Microstructure profiles were collected by a portable flux profiler (PFP) during calm and disturbed periods. Then, the vertical eddy diffusivity was estimated by three indirect methods. The estimated vertical eddy diffusivities varied more than one order of magnitude, from 4.7 x 10(-7) to 7.7 x 10(-6) m(2) s(-1). The comparison of results with previous buoyancy flux measurements and scaling arguments showed that the Dillon-Park's method is not appropriate and Osborn - Cox method performs better than Osborn method in the studied case. Furthermore, the low value of vertical eddy diffusivity within the thermocline suggests that within the thermocline of these lakes, diffusive vertical transport can be neglected.