The purpose of this study was to examine the genetic relationships among cold, salt and drought tolerance during seed germination in tomato by the analysis of response and correlated response to selection and by the identification and comparison of QTLs affecting these traits. Seeds of BC1 progeny of an interspecific cross between a slow-germinating Lycopersicon esculentum breeding line (NC84173; maternal and recurrent parent) and a fast-germinating L. pimpinellifolium accession (LA722) were evaluated for germination rate under cold, salt and drought stress. In each treatment, the most rapidly germinating seeds (the first 3% germinated = 30 seeds) were selected, grown to maturity under field conditions, and self-pollinated to produce BC1S1 progeny. Seed of the BC1S 1 progeny families from each selection experiment were evaluated for germination rate separately under nonstress (control), cold-stress, salt-stress, and drought-stress conditions, and their performances were compared with those of a nonselected BC1S1 population of the same cross. Results indicated that selection for rapid germination in each of the three stress treatments was effective and significantly improved progeny seed germination rate under all three stress conditions. The results suggested the presence of genetic relationships among cold, salt, and drought tolerance during seed germination in these tomato genotypes. To further examine such relationships, the selected BC1 plants from each treatment were subjected to marker analysis, using 119 RFLP markers. A trait-based marker analysis, which measures differences in marker allele frequencies between selected and nonselected populations, was used to identify marker-linked QTLs affecting each trait. A few QTLs were identified which affected germination rate under two or three stress conditions (stress-nonspecific QTLs) in addition to a few others which affected germination rate only under specific stress conditions (stress-specific QTLs). The overall results suggest that some genes affect the rate of tomato seed germination under different stress conditions.