The functional role of invariant chain in T-cell selection events and antigen presentation is well established. The invariant chain gene encodes differentially spliced isoforms, Ii31 and Ii41. The Ii41 isoform has been described to increase the efficiency of antigen presentation. We have analysed the effect of the Ii41 isoform on positive and negative selection of transgenic CD4 T cells with specificity for a natural self antigen (C5) which are crucially dependent on invariant chain for their development and functional antigen recognition. The data show that Ii41 fully substitutes for wild-type invariant chain in both positive and negative selection events during functional maturation of T cells with specificity for a natural, blood-borne self antigen.