Inositol polyphosphates are important eukaryotic second messengers with diverse roles in chromatin remodeling, telomere maintenance, mRNA export, and regulation of the phosphate starvation response. Despite strong research interest, relatively little is known regarding the regulation of inositol polyphosphate signaling in yeast or metazoans. Through studies incorporating quantitative phosphoproteomic analysis of kinase signaling pathways required for yeast pseudohyphal growth, we report here an unexpected regulatory interrelationship between inositol polyphosphate signaling and the cellular response to nitrogen stress. S. cerevisiae exhibits a dramatic growth response to nitrogen limitation, characterized by the transition from a vegetative yeast-like form to a filamentous form with chains of elongated pseudohyphal cells. Pseudohyphal growth is regulated through signaling networks encompassing MAPK and Snf1p pathways. We find that kinase-dead mutants of Ste11p, Ste7p, Kss1p, and Snf1p exhibit differential phosphorylation of the inositol polyphosphate kinases Arg82p, Vip1, and Kcs1p. Homozygous mutants deleted for IPK1, VIP1, and KCS1 display distinct pseudohyphal growth phenotypes under conditions of nitrogen limitation. Profiling of inositol polyphosphates upon growth in media with limited nitrogen reveals striking increases in the abundance of numerous inositol polyphosphate species, including IP3, IP7, and IP8. Further, deletion mutants of the pseudohyphal growth MAPK KSS1 and SNF1 exhibit altered profiles of IP7 isomers by HPLC analysis. In sum, we present data indicating regulatory control of inositol polyphosphates by Kss1p and Snf1p pathways, as well as results identifying regulatory control of pseudohyphal growth through inositol polyphosphate signaling. These findings are consistent with a role for inositol polyphosphate second messengers during the pseudohyphal growth transition, particularly with respect to downstream inositol polyphosphates and pyrophosphates that may function in a complex feedback control system with pseudohyphal growth regulators.