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Bioactive compounds such as ω-3 fatty acids and terpenes, have been associated with beneficial health effects; however, their solubility in the gastrointestinal tract and its bioavailability in the body are low. Nanoemulsions offer a viable alternative to disperse lipophilic compounds and improve their dissolution, permeation, absorption and bioavailability. Enzyme modified phosphatidylcholine (PC) with ω-3 fatty acids was used as emulsifier to stabilize oil-in-water nanoemulsions generated using ultrasound device. These systems were used as carriers of betulinic acid, which has reported anti-carcinogenic activity. Phospholipase-catalyzed modification of PC allowed the incorporation of 50 mol% of ω-3 fatty acids. Formation variables such as oil type and ultrasound amplitude had effects on nanoemulsion characteristics. Incorporation of betulinic acid affected globule size; however, betulinic acid nanoemulsions below 200 nm could be prepared. The conditions under which betulinic acid nanoemulsions were obtained using the modified phosphatidylcholine with the smaller globule size (91 nm) were 10% PC, 25% glycerol, medium chain oil and 30% amplitude for 12 min in the sonicator. Storage temperature had an effect on the stability of the nanoemulsions, at 5°C we observed the smallest growth in globule size. The use of olive oil decreased the globule size growth during storage of the nanoemulsion stabilized with modified phosphatidylcholine, although globule size obtained was greater than 200 nm. Medium pH had a significant effect on the nanoemulsions; alkaline pH values improved storage stability. These results provide useful information for using this type of carrier system on the formulation of products in the pharmaceutical or food industry.