The retention of human milk (HM) fat in nasogastric probes of infusion pumps can be observed during the feed of infants unable to suck at the mother’s breast. The lack of homogenisation of HM could contribute to the fat holding. Therefore, the present study evaluated (i) the influence of homogenisation on milk fat retaining in infant feeding probes and (ii) the in vivo effect of the homogenisation on lipid absorption by Wistar rats. The animals were fed with HM treated following two processing conditions, that is, pasteurised and homogenised–pasteurised. The animals were randomly subdivided into four experimental groups: water-fed (control), pasteurised milk, homogenised–pasteurised milk and pasteurised–skimmed milk. The results of food consumption, mass body gain, corporate metrics and plasma blood levels of total cholesterol did not show any difference (P < 0·05) among the three types of HM used in the experiments. The liver, intestine and intra-abdominal adipose tissue of the four groups of animals presented normal and healthy histology. The composition of fatty acids in the brain tissue of animals fed with homogenised HM increased when compared with the groups fed with non-homogenised HM. These values were 11·08 % higher for arachidonic acids, 6·59 % for DAH and 47·92 % for nervous acids. The ingestion of homogenised HM promoted higher absorption of milk nutrients. Therefore, the addition of the homogenisation stage in HM processing could be an alternative to reduce fat retention in probes and to improve the lipids’ absorption in the body.