This paper examines the effects of thermocapillary convection generated by a void or bubble on the self-diffusion measurement of molten indium in microgravity. The study is based on the thermophysical and geometrical configurations of the self-diffusion in liquid elements (SDLE) microgravity experiment. A transient finite element model of the diffusion capillary is presented. Numerical simulations of the transport processes in the diffusion capillary indicate that the concentration stratification in the enclosure is greatly modified by void-generated convection when small temperature non-uniformities are present in the system. The extent to which this modification can contaminate the diffusion data obtained by the Harned-Codastefano methodology is determined. In order to generalize the findings, results are summarized by relating the extent of the convective contamination of the diffusion data to the thermocapillary Reynolds number of the bubble and the Schmidt number of the system. © 2004 Elsevier B.V. All rights reserved.