Compared to the studies on acute irradiation of seeds, fewer studies have reported on the chronic irradiation of seedlings, especially in fruit-bearing vegetables. We examined the effects of chronic gamma irradiation on tomato (Solanum lycopersicum ‘Micro-Tom’) seedlings exposed to gamma rays (50, 100, 150, and 200 Gy) for 4 weeks. As the total dose of gamma rays increased, leaf length, trichome density, and seed number were reduced in the irradiated seedlings (M1). Additionally, a change in fruit shape was observed. Chronic gamma irradiation reduced the expression of two trichome-related genes and affected the expression levels of 11 reactive oxygen species (ROS)-related genes. We examined the transmittance of these effects using M2 plants. The trichome density and fruit shape were similar between M2 and control plants; however, a reduction in leaf length and seed number was detected in M2 plants. Interestingly, changes in the expression of four ROS-related genes (ZAT10, Mn-SOD, POD3, and RBOH1) found in M1 were detected in M2 plants. Thus, the changes in phenotype and gene expression induced by chronic gamma irradiation were transmitted to the next generation. Additionally, we found novel mutants from M2 plants, suggesting that chronic gamma irradiation may be considered in tomato mutation breeding.