Abstract The fractionation of apitoxin (bee venom) by means of a commercial 10 kDa ultrafiltration membrane was investigated aiming at the removal of phospholipase A2, the main allergenic substance. The feed content was varied from 1 to 50 g apitoxin/L, in deionized water, and caused changes in membrane flux and rejection, due to concentration polarization. The increase in pressure difference and stirring rate improved the flux through the membrane. The best result was achieved for 1 g apitoxin/L in feed stream, with a pressure difference of 220 kPa, and 750 rpm, with a permeate flux of 103 kg/m2h. The use of ultrafiltration was efficient to improve the permeate safety since biological tests revealed that the remaining enzyme lost its ability to catalyze the hydrolysis of phospholipids.