Tomato is one of the most economically and nutritionally important crops. It contains antioxidants such as lycopene, phenolics, vitamins E, C, and .-carotene at high levels. These traits are of interest to consumers and plant breeders for their health-related contributions. The main aim of plant breeding is to improve agronomically relevant traits by combining characters from different parental lines or their relatives. Genetic markers reveal these characters and other genetic differences between organisms. In this study both health-related and agronomically important traits were phenotypically identified by using 120 BC2F7, BC2F8, and BC2F9 IBLs. Also the lines were genotypically identified using the BC2F10 IBL population. A total of 66 COSII and 11 COS markers were positioned on the IBL map. A total of 103 QTLs were identified. Of these QTLs, 25 loci were identified for antioxidant traits: total water soluble antioxidant capacity, vitamin C content, lycopene and phenolic content. In addition, 78 QTLs were identified for agronomic traits: fruit weight, fruit shape, fruit firmness, stem scar size, external and internal color, locule number, fruit wall size, and soluble solid content. For most of the antioxidant QTLs, alleles from the S. pimpinellifolium parent were favorable. This result indicates that S. pimpinellifolium can be used as a source of high nutritional traits in order to improve elite tomato lines.