Changes in RNA secondary structure have been found to play important roles in translational regulation, protein synthesis, and mRNA splicing. In studies utilizing a 66 nucleotide RNA template with a stable hairpin structure, we have examined the effects of RNA secondary structure on HIV-1 reverse transcriptase activity. We identify several pause sites in the stem of the hairpin and show that these pause sites are correlated with the free energy of melting the next base pair in the stem. We also identify a pause site appearing in the loop of the hairpin and show that this is due to the rapid formation of a new hairpin structure occurring during the progress of DNA polymerization through the hairpin. The rapid change in RNA secondary structure to form the new hairpin selectively destabilizes the major hairpin and thereby accelerates the rate at which reverse transcriptase reads through RNA secondary structure.