In this study, we report on the relationship between individual antioxidant carotenoids, phenolic fractions, and flavonoids and attenuating NaCl toxicity in two contrasting varieties of lettuce (Lactuca sativa L., var. Verte and Romaine), as a means of developing more precise targets for lettuce breeding. In seedling leaves, carotenoid levels increased under NaCl stress in Verte, but remained unchanged in Romaine. Chlorogenic acid (CGA), a soluble polyphenol abundantly present in leaves, was the only phenolic acid that accumulated significantly in both varieties and was predominant under salinity. Remarkably, CGA was more prominent in Verte than Romaine at moderate salinity levels (100 mM). Foliar flavonoid levels were also differentially increased in both seedling types grown under 100 mM NaCl, but dropped significantly in both varieties under 200 mM NaCl. Germination, which was overall more salt-resistant in Romaine, was significantly increased under salt stress by application of low dosage (10–6 to10–5 M) of CGA to Verte, but not to Romaine. These results suggest that CGA is involved in modulating NaCl-induced oxidative-stress responses during seed germination in Verte.