Cauliflower mosaic virus (CaMV) strains CM1841 and W260 produced markedly different symptoms when inoculated onto turnips (Brassica campestris L. 'Just Right'). The CM1841 strain induced a mild degree of stunting of infected plants while strain W260 caused moderate to severe stunting. Although CM1841 was significantly milder than W260, it accumulated to a significantly higher concentration than W260 in systemically infected leaves. We constructed a series of hybrid viruses in order to map regions of W260 responsible for enhanced disease severity relative to CM1841 and to map regions of CM1841 responsible for higher virus accumulation. We found that the characteristic degree of stunting caused by a CaMV isolate is determined in a complex manner by viral genes that influence viral gene expression and viral genes that disrupt host metabolism. Genes I and VI influenced both virus concentration and stunting severity, suggesting that these regions affected disease severity primarily through their effect on gene expression. In addition, an interaction between genes IV and VI was observed which further indicated that stunting severity was influenced by differential accumulation of virus. In contrast, three regions of W260 influenced the stunting phenotype but had no effect, or a negative effect, on virus concentration. The three regions contained (1) portions of genes II and III, (2) gene IV, independent of gene VI, and (3) the 3' half of gene V and the 19 S promoter. These regions may influence stunting severity primarily by disrupting host metabolism. Additionally, some of the chimeric viruses induced systemic necrosis on leaves, a symptom that is not characteristic of either CM1841 or W260. The necrotic flecking symptom was caused by an interaction between a W260 DNA segment containing gene I and the 5' half of gene II and a CM1841 DNA segment containing the 3' half of gene II, gene III, and gene IV.