The study monitored the influence of genetic modification of cassava plants with NPT-II and GUS genes on starch content and physicochemical properties of transgenic starch for three cycles of vegetative propagation from 2010-2012. There were no significant (p>0.05) differences in the starch content and physicochemical properties among the three cycles of vegetative propagation. The NPT-II and GUS genes were strongly expressed in the vascular bundle, starch synthesizing and storage cells. The type of TME 12 variety (transgenic vs non-transgenic) has significant (p<0.05) influence on starch content, crude fibre, pasting viscosity and breakdown value. Starch content and crude fibre of non-transgenic plant (83.9%, 3.6%) were significantly (p<0.05) higher than that of transgenic plant (77.5%, 2.9%). Similarly, pasting viscosity and breakdown value (783.2 mPa s, 284.2 mPa s) of non-transgenic plants were greater than that of transgenic plant (621.0 mPa s, 133.1 mPa s) significantly. The implications of the findings on future genetic modification of cassava with NPT-II and GUS genes for starch quality improvement are discussed.