The nutritional value of egg yolk in terms of fat content and fatty acid (FA) composition is needed to evaluate their possible effect on human cardiovascular health and disease. This study determined the FA-based nutritional indices/ratios of egg yolks from 29 breeds belonging to seven poultry species (chicken, mallard, quail, Muscovy, guinea fowl, turkey, and ostrich) in a government poultry research station at Tiaong, Quezon, Philippines. At least four pooled samples (each consisting of four egg yolks) per breed were randomly collected and immediately frozen at –20 °C until analyzed for fat content and FA composition by gas chromatography. The major FAs in egg yolk with the highest proportions by weight of total FAs were oleic acid C18:1 n-9 (30.6–43.9%), palmitic acid C16:0 (22.2–54.4%), linoleic acid (LA) C18:2 n-6 (0.4–16.6%), and stearic acid C18:0 (4.0–12.1%). Compared to chicken and quail eggs, the mallard egg yolk seems to have more health benefits because of a lower LA to α-linolenic acid C18:3 n-3 (ALA) ratio (15.70: 1), atherogenicity (0.45), and thrombogenicity (0.91) – as well as higher yolk weight (22.7 g), fat content (31.8%), monounsaturated fatty acids (MUFA) to saturated fatty acids (SFA) ratio (1.73: 1), health-promoting index (2.20), and hypocholesterolemic/hypercholesterolemic ratio (2.26). Among mallard breeds, the egg yolks from Tsaiya and Pekin were superior to that from Itik-Pinas breeds. Egg yolk from other poultry species generally had lower FA-based nutritional values. Significant breed differences in fat content, FA composition, and nutritional indices/ratio were also reported for egg yolks from chicken, quail, and turkey.