Bioactive peptides present in foods may contribute to reducing the prevalence of chronic diseases. In foods, the peptides are usually released via enzymatic hydrolysis of proteins. In the paper, some selected analytical, chemometrics, and bioinformatics methods are presented, which are applied to evaluate the molecular and biological aspects of peptides derived from food proteins. There are also described methods to enhance the bioavailability of peptides as are some selected aspects of evaluating the safety. Understanding the molecular aspects of bioactive activity of peptides provides a basis for the progress in utilizing those compounds as components of foods that prevent the diet-related diseases.