On average, an end-stage renal disease patient will undergo hemodialysis (HD) three or four times a week for 4–5 h per session. Any minor imperfection in the extracorporeal system may become significant in the treatment of these patients due to the cumulative exposure time. Recently, air traps (a safety feature of dialysis systems) have been reported to be inadequate in detecting microbubbles and may even create them. Microbubbles have been linked to lung injuries and damage to the brain in chronic HD patients; therefore the significance of microbubbles has been revisited. Bubbles may originate at the vascular access sites, sites of local turbulent blood flow, the air trap, or in the bloodlines after priming with saline prior to use. In this paper, computational fluid dynamics is used to model blood flow in the air trap to determine the likely mechanisms of microbubble dynamics. The results indicate that almost all bubbles with diameters less than 50 μm and most of the bubbles of 50–200 μm pass through the air trap. Consequently, the common air traps are not effective in removing bubbles less than 200 μm in diameter.