The majority of the mass of a zebrafish zygote consists of the yolk, a lipid-rich structure that is gradually depleted by transport of its contents to the embryo as it develops into a free-feeding larva. Yolk lipids are packaged into lipoproteins in the YSL before being exported to the body of the developing zebrafish. Lipoproteins are lipid-transporting structures consisting of a neutral lipid interior bounded by a phospholipid (PL) and cholesterol monolayer, carrying one or more apolipoproteins. Apolipoproteins mediate interactions among lipoproteins, cellular receptors, and lipid-processing enzymes. The zebrafish genome contains analogs of every major human apolipoprotein, but there are some differences in patterns of expression and function. Due to the teleost genome duplication, zebrafish have multiple paralogs of each apolipoprotein gene. Human lipid metabolism genes with corresponding zebrafish paralogs discussed in this review are summarized in Table 1. There are 11 apolipoprotein genes in the apoB, apoA-IV, apoE, and apoA-I families, and all are expressed in the YSL (13) (Figure 1). Whole-mount in situ hybridization reveals that expression of some apolipoprotein genes is localized to subregions of the YSL, suggesting a previously uncharacterized compartmentalization of this structure. For example, mRNA encoding apoA-IV appears to be specific to the yolk extension at earlier stages (though different paralogs in this family are concentrated here at different points in development), while members of the other apolipoprotein families are expressed more evenly throughout the YSL (13). The significance of these potential YSL subdomains has yet to be described, but it is possible that there is a relationship to the regionalization of the developing intestine.