BACKGROUND: Sorghum (Sorghum bicolor L.) is used as a raw material for biofuels because it accumulates sugars at high levels in the stem. Lodging of sorghum occurs when the soil is wet and very high winds blow across the field. In root lodging, the roots are pulled loose from the soil, causing the plant to fall over. Lodging reduces the yield of nonstructural carbohydrates. It is not yet clear which genes show changes in expression when sorghum falls over. We compared whole-gene expression in the mature stems of intact and lodged sorghum plants, with a focus on comparisons from the perspective of differences in sugar accumulation or degradation. RESULTS: Lodging decreased sucrose content, starch content, and ratio of sucrose to total sugars in the stems of the sorghum cultivar SIL-05. Particular paralogs of SWEET and TMT family genes, which encode sucrose or hexose transporters, or both, were significantly highly expressed in intact or lodged sorghum stems. In intact stems, genes encoding the glucose-6-phosphate translocator, aquaporins, and enzymes involved in photosynthesis and starch synthesis were highly expressed. In lodged sorghum stems, expression of genes associated with sucrose or starch degradation or energy production was increased. Notably, expression of genes encoding enzymes catalyzing irreversible reactions and associated with the first steps of these metabolic pathways (e.g. INV, SUS, and hexokinase- and fructokinase-encoding genes) was significantly increased by lodging. Expression of SUT, SPS, and SPP was almost the same in intact and lodged sorghum. CONCLUSIONS: Specific paralogs of sucrose-associated genes involved in metabolic pathways and in membrane transport were expressed in the stems of sorghum SIL-05 at the full-ripe stage. Root lodging drastically changed the expression of these genes from sucrose accumulation to degradation. The changes in gene expression resulted in decreases in sugar content and in the proportion of sucrose to hexoses in the stems of lodged plants.