When gold nanorods are exposed to low-energy laser pulses, they can undergo shape transitions at temperatures below melting. In the present study such transitions are reproduced in molecular dynamics simulations of gold nanorods consisting of 10(3)-10(4) atoms. We find that the shape change is accompanied by a structural change. On the basis of the simulation results, a mechanism is suggested that explains the intermediate products and the internal defects of gold nanorods observed in laser heating experiments.