The sprout inhibition of onion and potato by low energy X-rays was investigated using a 160 kV X-ray irradiation system to determine optimal irradiation conditions. The sprouting of onion was effectively suppressed by irradiating 20 Gy at a depth of 3.2 mm from root side for small onion and at 8.0 mm depth for large onion, respectively. For potato, double-sided irradiation was necessary to irradiate the entire potato because the buds were distributed throughout the entire potato. Irradiation on double-sided at a depth of 8.0 mm with 50 Gy (60 Gy at 5.4 mm) effectively inhibited the sprouting. The throughput calculated to be 80.9 kg/h for large onion, 34.1 kg/h for small onion, and 9.9 kg/h for potato at a distance of 350 mm from the focal point of source. Dose uniformity (D max at surface/D min at 8.0 mm depth) of potato in case of double-sided irradiation was improved from 3.6 (182 Gy/50 Gy) to 1.2 (58 Gy/50 Gy) by using an aluminum 1.0 mm filter (F1) to cut off low energy X-rays, whereas the throughput capacity decreased from 9.9 kg/h to 7.4 kg/h.