Imaging isolated molecules in three dimensions with atomic resolution is important for elucidating complex molecular structures and intermediate states in molecular dynamics. This goal has so far remained elusive due to the random orientation of molecules in the gas phase. We show that three-dimensional structural information can be retrieved from multiple electron diffraction patterns of aligned molecules. The molecules are aligned impulsively with a femtosecond laser pulse and probed with a femtosecond electron pulse two picoseconds later, when the degree of alignment reaches a maximum.