Fruit shape is a quantitatively inherited character. In tomato, two major loci, sun and ovate, control fruit shape index, which is the ratio of fruit height over width. In this study, we measured many additional fruit shape features in three inter-specific F2 populations using the software application Tomato Analyzer. These populations were derived from varieties carrying elongated fruit but for which the major shape loci differed. We compared the effect of the major fruit shape loci with overall shape, as well as with the distal and proximal end shape features in each population. sun and ovate represented the largest effect on fruit shape in the Howard German and Sausage F2 populations, respectively. The largest effect QTL in the Rio Grande population carrying neither sun nor ovate, were fs8.1 on chromosome 8 and tri2.1/dblk2.1 on chromosome 2. These latter loci were also segregating in the other two populations, thus indicating common regions that control shape across the three populations. The phenotypic analyses showed that sun and ovate contributed to almost all aspects of shape such as the distal and proximal end features. In Rio Grande however, the largest effect QTL did not control all aspects of shape and the distal and proximal features were distinctly controlled in that population. Combined, our results implied that within the cultivated tomato germplasm pool the largest effect on elongated fruit shape was controlled by a combination of the loci sun, ovate, fs8.1 and tri2.1/dblk2.1.