The purpose of this study was to determine the genetic relationship between salt tolerance (ST) during seed germination (SG) and vegetative stage (VS) in tomato by comparing quantitative trait loci (QTLs) which contribute to ST at these two developmental stages. A total of 145 F9 recombinant inbred lines (RILs) of a cross between a salt-sensitive Lycopersicon esculentum breeding line (NC84173) and a salttolerant L. pimpinellifolium accession (LA722) were evaluated in replicated trials for ST during SG (time to 50% germination) and VS (plant survival under salt stress). There was no significant phenotypic correlation (r = 0.03) between the rate of SG and plant survival under salt stress. The RILs were genotyped for 129 restriction fragment length polymorphism (RFLP) markers and 62 resistance gene analogs (RGAs), covering 1505 cM of the 12 tomato chromosomes with an average marker distance of 7.9 cM. Marker analysis identified 9 QTLs for ST during SG and 8 QTLs for ST during VS. Mostly different QTLs were identified for ST during these two stages, supporting the suggestion that different genetic and physiological mechanisms contribute to ST during SG and VS. However, simultaneous improvement of ST at these two stages should be possible through the use of marker-assisted selection.