A naturally occurring splice variant of hepatocyte growth factor (HGF) lacks a 5-amino acid sequence in the first kringle domain. Comparison of HGF and the deletion variant (dHGF) revealed that the deletion significantly altered the biological activities, solubility, and immunological property of HGF. HGF was respectively about 20-, 10-, and 2-fold more potent than dHGF in the stimulation of DNA synthesis in human umbilical vein endothelial cells, human aorta smooth muscle cells, and NSF-60 (murine myeloblastic cells). Conversely, dHGF was respectively about 3-, 2-, and 2-fold more potent than HGF in the stimulation of DNA synthesis in LLC-PK1 (pig kidney epithelial cells), OK (American opossum kidney epithelial cells), and rat hepatocytes. Moreover, HGF was over 70-fold more soluble than dHGF in PBS. Several monoclonal antibodies raised against dHGF recognized only dHGF and neither HGF nor reduced dHGF, demonstrating that the deletion caused a tertiary structural change. The structural change in HGF may be responsible for its altered biological activities and solubility.