Gene expression analysis on laser capture microdissected samples can be hampered because of the small sample size. The interference of PCR inhibitors increases with smaller sample size. Real-time reverse transcription PCR (RT-PCR) is usually performed directly after the reverse transcription step, enabling PCR inhibitors to remain in the complementary DNA (cDNA). A protocol was optimized for real-time RT-PCR with SYBR Green I. The introduction of an additional cDNA purification step after reverse transcription removed PCR inhibitors, making the reaction more efficient.