In renal physiology, ultrafiltration occurs at the barrier between the blood and the filtrate in the glomerular capsule (Bowman's capsule) in the kidneys. As in nonbiological examples of ultrafiltration, pressure (in this case blood pressure) and concentration gradients lead to a separation through a semipermeable membrane (provided by the podocytes). The Bowman's capsule contains a dense capillary network called the glomerulus. Blood flows into these capillaries through the afferent arterioles and leaves through the efferent arterioles.

The high hydrostatic pressure forces small molecules in the tubular fluid such as water, glucose, amino acids, sodium chloride and urea through the filter, from the blood in the glomerular capsule across the basement membrane of the Bowman's capsule and into the renal tubules. This process is called ultrafiltration; the resulting fluid, virtually free of large proteins and blood cells, is referred to as glomerular filtrate, or ultrafiltrate. Further modification of ultrafiltrate, by reabsorption and secretion, transforms it into urine.

Glomerular pressure is about 75 millimeters of mercury (10 kPa). It is opposed by osmotic pressure (30 mmHg, 4.0 kPa) and hydrostatic pressure (20 mmHg, 2.7 kPa) of solutes present in capsular space. This difference in pressure is called effective pressure (25 mmHg, 3.3 kPa).

In hemodialysis centers, ultrafiltration takes place in a hemofilter on the hemodialysis machines, when the blood pressure is greater than the dialysate pressure (difference = transmembrane pressure (TMP)). This removes fluid from the blood while keeping its blood cells intact.