An increasing interest in organic agriculture for food production is seen throughout the world and one key reason for this interest is the assumption that organic food consumption is beneficial to public health. The present paper focuses on the background of organic agriculture, important public health related compounds from crop food and variations in the amount of health related compounds in crops. In addition, influence of organic farming on health related compounds, on pesticide residues and heavy metals in crops, and relations between organic food and health biomarkers as well as in vitro studies are also the focus of the present paper. Nutritionally beneficial compounds of highest relevance for public health were micronutrients, especially Fe and Zn, and bioactive compounds such as carotenoids (including pro-vitamin A compounds), tocopherols (including vitamin E) and phenolic compounds. Extremely large variations in the contents of these compounds were seen, depending on genotype, climate, environment, farming conditions, harvest time, and part of the crop. Highest amounts seen were related to the choice of genotype and were also increased by genetic modification of the crop. Organic cultivation did not influence the content of most of the nutritional beneficial compounds, except the phenolic compounds that were increased with the amounts of pathogens. However, higher amounts of pesticide residues and in many cases also of heavy metals were seen in the conventionally produced crops compared to the organic ones. Animal studies as well as in vitro studies showed a clear indication of a beneficial effect of organic food/extracts as compared to conventional ones. Thus, consumption of organic food seems to be positive from a public health point of view, although the reasons are unclear, and synergistic effects between various constituents within the food are likely.