The Per-Arnt-Sim (PAS) domains of hypoxia-inducible transcription factors (HIF) mediate heterodimer formation between the HIF-alpha forms that are induced in the event of cellular hypoxia and the constitutive variants. Previous efforts toward structural characterization of the HIF-1 alpha PAS domains were limited by protein stability. Using homology modeling based on the published crystal structure of the PAS-B domain of the homologous protein HIF-2 alpha in complex with the partner HIF-beta (also known as ARNT), we have identified a variant of HIP-1 alpha with improved solubility, monodispersity, and stability. Purified solutions of the PAS-B domains of HIP-1 alpha and HIF-2 alpha differ in their propensity for homodimer formation. In an attempt to understand the structural basis for this difference, and to document the structural changes that accompany homodimer formation, we have undertaken a comparative NMR study of the PAS-B domains of HIF-1 alpha and HIF-2 alpha and mutants of HIF-1 alpha that mimic the behavior of HIP-2 alpha. The NMR spectra of all of these domains are very similar, consistent with the similarity of their amino acid sequences. However, the greater propensity of the HIP-1 alpha PAS-B domain to form dimers as the concentration was increased allowed us to determine the site of homodimerization and pointed toward possible sequence changes in HIP-1 alpha that might discourage the formation of homodimers.