Shiga toxin 1 (Stx1) and Shiga toxin 2 (Stx2) differ regarding receptor affinity, cellular toxicity and clinical outcome. To this date, it is not clarified in detail why the subtypes display these differences. Even though the crystal structures of Stx1 and Stx2 share overall similarities, significant differences were found in the C-terminal end of the A-subunits. The aim of this study was to investigate the role of the C-terminal end of the A-subunit in complex stability and retrograde transport by generating truncated mutants where 2, 4, 6 and 8 amino acids were removed from the C-terminal end of Stx1A and Stx2A. The results obtained show that removal of 6 or 8 amino acids from the Stx1A C-terminus abolishes the AB5 complex integrity, while removing up to 8 amino acids from Stx2A does not affect the complex in vivo (in the bacteria). We also present results showing different levels of A1-subunit in HeLa cells after exposure to Stx1, Stx2 and their truncated mutants.