In the genomic era, the routine collection of accurate phenotypes remains a major challenge, especially for difficult- or expensive-to-record traits such as health, fertility and environmental footprint. Previous research demonstrated the opportunity of using milk biomarkers as predictors of these traits. Hence, milk biomarkers can be useful in the prediction of genetic merit for direct fertility, health, and environmental footprint traits as long as they are easier to measure, heritable, and genetically correlated. Recently, mid-infrared (MIR) spectrometry was recognized as a rapid and cost-effective tool to collect routinely a wide range of novel milk phenotypes including fine milk composition, milk technological properties and cow’s physiological status. Investigations on the genetic relationship between fertility and milk phenotypes indicated that milk phenotypes related to the negative postpartum energy balance and the body fat mobilization (e.g. fat to protein ratio, fatty acids profile) could be used to improve fertility. Moreover, contents in milk of ketone bodies could be useful for breeding cows less susceptible to ketosis. Although the genetic association of milk phenotypes other than somatic cell count and mastitis should be further investigated, a wide range of traits (e.g. lactoferrin, minerals, citrate) are worth to be considered as potential indicators of udder health. Finally, fatty acids can be used as predictors of methane production and MIR-prediction of methane production has been demonstrated as genetically variable and heritable. Further studies will allow to (1) grasp underlying associations among novel milk phenotypes and health, fertility, and environmental footprint traits, (2) conduct genetic and genomic studies for these traits, and (3) include these traits in broader breeding strategies.