Bull fertility is crucial for efficient, profitable, and sustainable agriculture of cattle. Despite the fact that the uses of sperm from low fertility bulls cause millions of dollars economic losses, conventional methods available to accurately predict bull fertility are still of limited use. Although breeding bulls produce billions of sperm mostly with normal motility and morphology, some bulls are afflicted with poor fertility due to molecular or cellular defects in the sperm. Sperm functional genome including transcriptome, proteome, and metabolome influence bull fertility. Through high throughput screening methods of metabolomics, specific small molecules have been described both for seminal plasma and sperm. Compared to sperm, seminal plasma contains much higher numbers and levels of metabolites. Although the identities and functions of many of these metabolites are known, such knowledge is still yet to be generated for a greater number of metabolites of sperm and seminal plasma. Once validated as fertility markers, sperm, and seminal plasma metabolites can be used to evaluate semen quality and predict bull fertility, and/or used in assisted reproductive technologies. This review describes the possibility to use small molecules (in the review called metabolites) as fertility predictors.