The invariant chain protein is intracellularly associated with class II major histocompatibility proteins. In many cases, the expression of these molecules appears to be regulated in a similar manner. Contained with the promoter of the invariant chain gene are sequences (X and Iγ1) that are similar to the X and Y box elements of class II genes, suggesting that these sequences might be involved in its regulation. DNase I footprinting reveals additional cis-acting elements (Iγ2 and Iγ3) that contain sequence similarities to NF-κB and/or H2TF1/KBF1 recognition sequences. A series of fusion constructs with the chloramphenicol acetyltransferase reporter gene were used to analyze the role of these sequences (Iγ1, Iγ2, Iγ3, and X and Y elements) in both normal and mutant B lymphocytes. These data suggest the likelihood of multiple X box proteins in B cells, which can act as both negative and positive regulatory factors.