MHC class II deficiency is a severe primary immunodeficiency characterized by the absence of Major Histocompatibility Complex class II gene expression. It is genetically heterogenous and can result from defects in several different transacting regulatory factors required for transcription of MHC class II genes. Cell lines from MHC class II deficiency patients have been assigned to three complementation groups (A, B, C). An in vitro generated cell line (6.1.6) was reported to be the sole representative of a fourth group (group D). The molecular defect in 6.1.6 resides in the recently cloned RFXAP gene. Direct complementation experiments and mutation analysis were performed with cell lines from several MHC class II deficiency patients in which the affected gene had not been identified. These experiments have allowed us to define a previously unrecognized MHC class II deficiency complementation group containing patients having mutations in the RFXAP gene.