Salinity stress is one of the most serious factors limiting the productivity of agricultural crops. The aim of this study was to assess inter-cultivar (intraspecific) variation for salinity tolerance in six Korean rapeseed (Brassica napus L.) cultivars at the seedling stage. The effect of three different salinity stress levels (EC 4, 8, and 16 $dS{\cdot}m^{-1}$) on seedlings of six cultivars was investigated through leaf size, leaf dry weight, and leaf chlorosis. At the highest salinity level (16 $dS{\cdot}m^{-1}$), the mean decrease of leaf dry weight in 'Sunmang', 'Tammi', 'Tamla', 'Naehan', 'Youngsan', and 'Halla' was about 56.2, 56.9, 78.4, 79.3, 77.4, and 80.9%, respectively. 'Tammi' and 'Sunmang' showed much less reduction in leaf dry weight than all the other cultivars. In addition, diluted seawater treatments increased the occurrence of leaf chlorosis in six cultivars. At EC 8 and 16 $dS{\cdot}m^{-1}$, 'Naehan', 'Youngsan', and 'Halla' showed a higher level of leaf chlorosis than 'Tammi' 'Sunmang', and 'Tamla'. On the basis of these results, six cultivars were placed into salinity-tolerant and sensitive groups. 'Tammi' and 'Sunmang' were the salinity-tolerant cultivars, while 'Naehan', 'Halla', 'Youngsan', and 'Tamla' were the salinity-sensitive cultivars. 'Tammi' and 'Naehan' rated as the most tolerant and most sensitive cultivar, respectively. To further analyze protein expression profiles in 'Tammi' and 'Naehan', 2-D proteomic analysis was performed using the plants grown under diluted seawater treatments. We identified eight differentially displayed proteins that participate in photosynthesis, carbon assimilation, starch and sucrose metabolism, amino acid metabolism, cold and oxidative stress, and calcium signaling. The differential protein expressions in 'Tammi' and 'Naehan' are likely to correlate with the differential growth responses of both cultivars to salinity stress. These data suggest that 'Tammi' is better adapted to salinity stressed environments than 'Naehan'.