The effect of ultrafiltration and diafiltration on the distribution of the calcium phosphate clusters of the casein micelle was investigated using Small Angle Neutron Scattering (SANS). In the case of ultrafiltration, fresh skim milk was subjected to concentration using membrane filtration up to 5× its original volume, the retentate was rediluted with its corresponding serum and subsequently dialyzed against reconstituted milk powder dispersed in D2O/H2O (UF 5×(D)). In the case of diafiltered samples, the samples were concentrated adding water (diafiltration) at two different levels (DF 2·5× or DF 5×) and then redispersed with D2O/H2O. In the DF 5× case, the serum components were diluted to less than 1% of their original concentration. For analysis, all samples had the same volume fraction of dispersed casein micelles (φ=0·1), which is that of the control, unprocessed skim milk. A peak in the SANS data was observed in fresh skim milk at a scattering vector, qo, of 0·034 Å−1 (directly proportional to the reciprocal characteristic length), in agreement with previous literature results. Neutron data on the ultrafiltered, UF 5×(D) and diafiltered, DF 2·5× and DF 5× milk samples showed a progressive decrease in the intensity of the peak but invariance in qo. These results, combined with the determination of soluble and insoluble calcium in the samples, suggest a progressive and irreversible removal of calcium from within the micelle during membrane filtration of milk. Using SANS it was possible to clearly show changes in the micellar calcium clusters that may not otherwise be fully determined by only measuring the amount of total and insoluble calcium in milk.