Bisphenol-A polycarbonate/eugenol-siloxane copolymers were fractionated at the preparative scale by the continuous polymer fractionation (CPF) technique. It is the first example of copolymer fractionation by CPF. The distribution of siloxane species across the fractions was assessed for copolymers differing in initial siloxane concentration and block length. On- and off-line combinations of size exclusion chromatography and infrared spectroscopy were used to analyze chemical composition (CC) of the unfractionated samples across the molecular weight distribution enabling comparison with the fractions. A polycarbonate-siloxane copolymer containing 10 wt% of very short siloxane blocks (dp = 2) was fractionated solely according to molecular weight (MW). By contrast, a copolymer containing 5 wt% siloxane blocks with a larger degree of polymerization (dp = 23) was fractionated according to MW, as well as to CC. This 'chemical drift' effect for the larger siloxane block length can be ascribed to large solubility differences of low MW chains, which drastically vary in composition according to the (small) number of siloxane blocks they contain.