Salt stress is one of the key abiotic stresses threatening future agricultural production and natural ecosystems. This study investigates the salt stress response of two rice seedlings,whichwere screened from28 Kenya rice cultivars. A proteomic analysis was carried out andMapman bin codes employed in protein function categorization. Proteins in the redox, stress, and signaling categories were identified, andwhose expression differed between the salt tolerant and the salt sensitive samples employed in the present study. 104 and 102 root proteins were observed as significantly altered during salt stress in the tolerant and sensitive samples, respectively and 13 proteins were commonly expressed.Among the 13 proteins, ketol-acid reductoisomerase protein was upregulated in both 1 and 3 days of salt treatment in the tolerant sample, while itwas down-regulated in both 1 and 3 days of salt treatment in the sensitive sample. Actin-7, tubulin alpha, V-type proton ATPase, SOD (Cu-Zn), SOD (Mn), and pyruvate decarboxylasewere among the observed salt-induced proteins. In general, this study improves our understanding about salt stress response mechanisms in rice.