Breeding and biotechnological approaches are currently used to increase the content of specific bioactive components of plants, but the manipulation of plant metabolism is still not easy to address. There is an increasing awareness that multiple genetic and environmental factors affect production and accumulation of bioactive compounds, but these factors are rarely taken into account when fruit is marketed. Rigorous and unprejudiced evaluation of scientific evidence requires a defined set of criteria and methods of evaluation, particularly when breeding and biotech programs are aimed of producing new varieties with improved nutritional values combined with high plant production efficiency and fruit quality. In order to develop new genotypes and commercial cultivars the availability of new sources of Quality Attributes (QA) and Nutritional Attributes (NA) should be explored. In the strawberry, wild species such as F. virginiana glauca and F. vesca are good sources of bioactive compounds, but in raspberries the introduction of the wild germplasm (R. parvifolium) did not improve the nutritional quality of fruit. The methods available for detecting fruit TAC, combined with TPH and other quality parameters such as sugars, total acidity and fruit color, can be proposed as excellent tools for developing a fast and reliable program for screening large breeding populations for high nutritional quality genotypes. Furthermore, NA can represent a useful tool to facilitate analysis of "substantial equivalence" of transgenic and control derived fruit.