Nature, as well as the human body, contains an abundant quantity of organic molecules. This textbook describes selected oxygen, sulfur, nitrogen derivatives of hydrocarbons, heterocyclic compounds of their reactions, which are important in the human body or are found in pharmaceutical active substances, poisons, foodstuffs and heat-treated food. The last part of the textbook describes the isomerism of organic compounds, which enables dynamic changes in the structure of molecules that have different properties. Nature is filled with different plants and animals and is the first laboratory to produce bioactive organic natural compounds. These compounds are compatible with human cells and are applicable as therapeutic medicine. There is an effort to reproduce natural molecules in chemical laboratories, but they cannot be as perfect as the natural ones. Synthetic molecules can serve as a model for multiple studies, but there still does not exist a magic panacea pill or a perfect copy of nature, for the treatment of various diseases. Knowledge about the regenerative and toxic effect of medicinal substances in dependence on their structure (type and number of substituents) is very important for the understanding of their role in modulation of health and disease in dependence on their concentration.