Effects of structural defects on thermal transport in carbon nanotubes are revealed through nonequilibrium molecular-dynamics simulations with the Tersoff-Brenner bond-order potential. The thermal conductivity of carbon nanotubes decreases rapidly down to 25 % with only 1 % vacancy defects. By performing thermal annealing, the vacancy defects are mainly transformed into 5-6 defects consisting of pentagon-hexagon pairs, and the reduced thermal conductivity due to vacancy defects is increased by 4-7 %. This improvement in thermal conductivity can be understood from the result that the thermal resistance of the 5-6 defects is smaller than that of the vacancy defects. [DOI: 10.1380/ejssnt.2006.239]