The molecular basis for the defective expression of the mouse class II E beta genes in the H-2w17, H-2q, and H-2f haplotypes has been examined. The results of nuclear run-on transcription and S1 nuclease digestion assays demonstrate that E beta transcription is normal in these haplotypes. Northern blot analyses reveal reduced amounts of E beta RNA of both normal and aberrant size in the w17 and q haplotypes; an even more reduced level of E beta RNA of normal size was detected in the f haplotype. In the preceding study, we reported that the only defect detected in the E beta w17 gene is a single nucleotide insertion in the 5' RNA splice site of the first intervening sequence. S1 nuclease analysis of E beta w17 RNA indicates that splicing at this site is aberrant. One major cryptic RNA splice site is used, leading to reduced amounts of aberrantly processed RNA. Limited use of the mutated splice site and of a second cryptic site also is detected. In all three cases, stop codons in the resulting RNA would prevent their translation. The molecular defect in E beta q appears identical to that of E beta w17. In the f haplotype, even more reduced levels of E beta RNA of both normal and aberrant sizes are found. We thus show that in the three defective E beta alleles, two distinct defects are responsible for the absence of E beta protein synthesis; both of these defects affect RNA processing.