In a shaft arrangement structure of an engine which is provided with a crank case divided into upper and lower two members, forms a transmission room accommodating a transmission within the crank case, and utilizes a lower portion of the transmission room as an oil reservoir chamber, an input shaft of the transmission is positioned above a line connecting an axis of the crank shaft of the engine and an axis of the output shaft of the transmission as seen in an axial direction. An angle formed between a first segment connecting the axis of the crank shaft and the axis of the input shaft and a center line of a cylinder of the engine above the axis of the crank shaft is acute.