We used electron tomography to determine the three-dimensional (3D) structure of integrin αIIbβ3 in the active state. We found that we obtained better density maps when we reconstructed a 3D volume for each individual particle in the tilt series rather than to extract the particle-containing subvolumes from a 3D reconstruction of the entire specimen area. The 3D tomographic reconstructions of 100 particles revealed that activated αIIbβ3 adopts many different conformations. An average of all the individual 3D reconstructions nicely accommodated the crystal structure of the αVβ3 headpiece, confirming the locations assigned to the α- and β-subunit in the density map. The most striking finding of our study is the structural flexibility of the lower leg of the β-subunit as opposed to the conformational stability of the leg of the α-subunit. The good fit of the atomic structure of the βI domain and the hybrid domain in the active state showed that the hybrid domain swings out, and most particles used for tomography are in the active state. Multivariate statistical analysis and classification applied to the set of 3D reconstructions revealed that more than 90% reconstructions are grouped into the classes that show the active state. Our results demonstrate that electron tomography can be used to classify complexes with a flexible structure such as integrins.