Genetic factors strongly influence the intake and preference for sugar and saccharin solutions in inbred mouse strains. The present study determined if genetic variance also influences the learned preferences for flavors added to sugar solutions. Conditioned flavor preferences (CFP) are produced in rodents by adding a flavor (CS+) to a sugar solution and a different flavor (CS−) to a saccharin solution (CS−) in one-bottle training trials; the CS+ is subsequently preferred to the CS− when both are presented in saccharin solutions in two-bottle tests. With some sugars (e.g., sucrose), flavor preferences are reinforced by both sweet taste and post-oral nutrient effects, whereas with other sugars (e.g., fructose), sweet taste is the primary reinforcer. Sucrose and fructose were used in three experiments to condition flavor preferences in one outbred (CD-1) and eight inbred strains which have “sensitive” (SWR/J, SJL/J, C57BL/10J, C57BL/6J) or “sub-sensitive” (DBA/2J, BALB/cJ, C3H/HeJ, 129P3/J) sweet taste receptors (T1R2/T1R3). Food-restricted mice of each strain were trained (1 h/day) to drink flavored 16% sucrose (CS+16S, Experiment 1), 16% fructose (CS+16F, Experiment 2) or 8% fructose + 0.2% saccharin (CS+8F, Experiment 3) solutions on five alternate days and a differently flavored saccharin solution (0.05% or 0.2%, CS−) on the other five alternating days. The CS+ and CS− flavors were presented in 0.2% saccharin for two-bottle testing over six days. All strains preferred the CS+16S to CS− although there were significant strain differences in the magnitude and persistence of the sucrose preference. The strains also differed in the magnitude and persistence of preferences for the CS+16F and CS+8F flavors over the CS− with two strains failing to prefer the fructose-paired flavors. Sucrose conditioned stronger preferences than did fructose which is attributed to differences in the taste and post-oral actions of the sugars. These differential training intakes may not have influenced the sucrose-CFP because of the post-oral reinforcing actions of sucrose. Overall, sweet sensitive and sub-sensitive mice did not differ in sucrose-CFP, but unexpectedly, the sub-sensitive mice displayed stronger fructose-CFP. This may be related to differential training intakes of CS+ and CS− solutions: sweet sensitive mice consumed more CS− than CS+ during training while sub-sensitive mice consumed more CS+.