Microbubbles have been detected in the human circulation of end-stage renal disease patients who are treated by hemodialysis throughout the past decade as a result of advanced ultrasound and Doppler technology. These detection tools uncovered signals of microbubbles, which originate in extracorporeal lines and tubing of hemodialysis machine, circulate in the blood stream until lodging in the capillary bed of various organs, mainly the lungs. During its course within the capillary, a bubble abrades the glycocalyx layer lining the surface of the vessels and thereafter obstructs blood flow through the capillary. This causes tissue ischemia, inflammatory response, and complement activation. Aggregation of platelets and clot formation occurs as well, leading to further obstruction of the microcirculation and subsequent tissue damage. In this review, we describe the biological and clinical effects of microbubbles during hemodialysis and discuss management with regard to prevention and treatment.