To study the role of trace elements for the quality and nutritional value of bovine milk, the distribution of selenium, zinc, and copper in whey was investigated using a method linking size exclusion chromatography to inductively coupled plasma mass spectrometry (SEC-ICP-MS). Three major peaks were detected for selenium, two peaks for zinc, and five peaks for copper. More than 65% of the selenium was found in protein fractions, mainly in fractions coinciding with the major whey proteins beta-lactoglobulin and alpha-lactalbumin. All zinc was associated with low molecular weight compounds (<5 kDa) and one of these compounds was probably citrate. More than 60% of the copper eluted in protein fractions and two of the five major peaks probably contained metallothionein and citrate. This method was used to compare milk and whey produced by organic and conventional feeding procedures. The selenium content in whey and desalted milk produced using organic regimens was significantly lower than that in conventional samples. Moreover, the proportion of selenium in protein fractions of organic whey was significantly smaller than that in conventional whey, but the distributions of zinc and copper did not differ. This study showed that with the SEC-ICP-MS technique the distribution profiles of several trace elements in whey could be studied in the same run and that the selenium profile differed in whey produced by organic and conventional procedures.