Transcripts encoded by six of the homeotic lethal complementation groups within the Antennapedia and bithorax gene complexes (ANT-C and BX-C) accumulate primarily in nonoverlapping regions of the embryonic central nervous system (CNS). It has been previously proposed that the maintenance of these selective patterns of expression involve hierarchical cross-regulatory interactions among ANT-C and BX-C loci. Selective expression of the ANT-C and BX-C also involves regulation by a number of unlinked genetic loci, including the Polycomb (Pc) locus. Here we show that the ANT-C and BX-C transcript distribution patterns are dramatically altered in the CNS of Pc- embryos. We discuss these altered patterns of expression in the context of different models for the spatial regulation of ANT-C and BX-C gene expression.