Opitz syndrome (OS) is a human genetic disease characterized by deformities such as cleft palate that are attributable to defects in embryonic development at the midline. Gene mapping has identified OS mutations within a protein called Midi. Wild-type Midi predominantly colocalizes with microtubules, in contrast to mutant versions of Midi that appear clustered in the cytosol. Using yeast two-hybrid screening, we found that the alpha4-subunit of protein phosphatases 2A/4/6 binds Midi. Epitope-tagged alpha4 coimmunoprecipitated endogenous or coexpressed Midi from COS7 cells, and this required only the conserved C-terminal region of alpha4. Localization of Midi and alpha4 was influenced by one another in transiently transfected cells. Midi could recruit alpha4 onto microtubules, and high levels of alpha4 could displace Midi into the cytosol. Metabolic P-32 labeling of cells showed that Midi is a phosphoprotein, and coexpression of full-length a4 decreased Midi phosphorylation, indicative of a functional interaction. Association of green fluorescent protein-Midi with microtubules in living cells was perturbed by inhibitors of MAP kinase activation. The conclusion is that Midi association with microtubules, which seems important for normal midline development, is regulated by dynamic phosphorylation involving MAP kinase and protein phosphatase that is targeted specifically to Midi by alpha4. Human birth defects may result from environmental or genetic disruption of this regulatory cycle.