To speed up the molecular analysis of cassava transgenic plants, we developed real-time polymerase chain reaction (PCR)-based methods that could be implemented as a tool in the primary scrutiny of putative transgenic plants. We tested for the presence of transgenes, estimated copy number, and quantified messenger RNA (mRNA) levels of genes introduced through Agrobacterium. Copy numbers for the genes ß-glucuronidase and hygromycin phosphortransferase were estimated in 15 transgenic lines.