Two recent theoretical models, Bai et al (2004, 2007) and Tadigotla et al (2006), formulatedthermodynamic explanations of sequence-dependent transcription pausing by RNApolymerase (RNAP). The two models differ in some basic assumptions and therefore makedifferent yet overlapping predictions for pause locations, and different predictions on pausekinetics and mechanisms. Here we present a comprehensive comparison of the two models.We show that while they have comparable predictive power of pause locations at low NTPconcentrations, the Bai et al model is more accurate than Tadigotla et al at higher NTPconcentrations. The pausing kinetics predicted by Bai et al is also consistent withtime-course transcription reactions, while Tadigotla et al is unsuited for this type ofkinetic prediction. More importantly, the two models in general predict differentpausing mechanisms even for the same pausing sites, and the Bai et al modelprovides an explanation more consistent with recent single molecule observations.