The nuclear receptor superfamily mediates the regulatory activities of many hormones, nutrients and metabolites on the homeostasis and physiology of cells and tissues. Classically, ligand binding induced the ability of nuclear receptors to modulate the transcription rate of target genes (genomic effects), which led to consider them as ligand-activated transcription factors. Later, rapid actions of nuclear receptor ligands were reported that did not involve changes in gene expression. These (non-genomic) effects have been attributed in some cases to receptors different to those mediating gene transcription but most evidences indicate that they result from the activity of a population of nuclear receptor molecules acting outside the cell nucleus. Recent studies on estrogen and vitamin D, and their receptors (ERalpha/beta, VDR) support now the idea that non-genomic and genomic effects may integrate in a unique mode of action of nuclear receptor ligands, in which the non-genomic effects constitute signaling pathways required for the effects at the genome level. Here, we will discuss these novel findings and also those indicating transcriptional regulation through ligand-dependent and -independent crosstalk of nuclear receptors with beta-catenin or VDR-interacting repressor (VDIR).