Inclusion of secondary or ‘functional’ traits in breeding objectives began in earnest only in the late 1990. By 2009, production traits accounted for less than 50% of the indices in most advanced countries. Breeding for fertility, health traits and herd life (HL) was hindered due to difficulty of measurement and analysis and generally low heritability. Statistical methods have been developed that overcome these problems. The advantages and limitations of breeding for disease traits and HL via selection on correlated traits and via cross-breeding are discussed. Methodologies for detection and analysis of the actual segregating genes that affect functional traits are presented.