A line with genetic changes that was obtained from selfed seeds of the scion of an intraspecific pepper graft was used as a source of new characteristics in this breeding experiment. Five new variant lines and several sublines were bred by the use of this graft-induced variant strain and two other cultivars. Gradual introduction of the desired quantitative traits and selection resulted in combinations which significantly outperform the parental lines. Our breeding aim was to combine the two-lobed fruit shape that is characteristic for the graft-induced variants with thick pericarp, high sugar content, large fruit size, and significantly reduced or eliminated pungency in the new variants. A bushy plant type, typical for the graft-induced variants could be maintained in some selected sublines. The use of the three different genotypes resulted in many favorable combinations of quantitative traits, and lines were selected with the most valuable new characteristics. However, not all of these expressed the two-lobed fruit apex of the graft-induced variants. Our results reveal that the new characteristics which are induced by grafting are stable, new traits, and can be used as a novel genetic source in the breeding of pepper.