Casein and whey protein fractions of milk obtained from 47 ewes of five breeds or crossbreeds (Awassi, Merino, East Friesian x Merino, Awassi x Merino and Awassi x East Friesian) were analysed by capillary electrophoresis (CE). The experiments were performed on a Beckman P/ACE (TM) system 5510 with an uncoated fused-silica capillary and a low pH buffer containing urea and a polymeric additive. The four major caseins (alpha(s1)-, alpha(s2)-, beta- and kappa-casein) in an acid precipitate were well separated, as were the two whey proteins, alpha-lactalbumin (alpha-La) and beta-lactoglobulin (beta-Lg). The electromigration of the proteins was in the order of alpha-La, beta-Lg, alpha(s2)-CN, alpha(s1)-CN, kappa-CN and beta-CN. The milk samples were composed of the same variant of alpha-La and two different genotypes (A and B) of beta-Lg while the beta-Lg AB genotype was evident in the milk of some animals. The alpha(s1)-CN fractions displayed considerable heterogeneity with at least 4 different peaks, representing 4 different variants. A fifth peak, corresponding to the Welsh variant (or alpha(s1)-CN D), was present in 90% of the ewes' milk samples. The kappa-CN fraction was resolved as a single peak, while the beta-CN revealed significant heterogeneity with 3 variants. It appears that the presence of the alpha(s1)-CN Welsh variant in Merino ewe and its crosses with Awassi and East Friesian ewes adversely affected milk composition and yield. (c) 2004 Swiss Society of Food Science and Technology. Published by Elsevier Ltd. All rights reserved.