The effect of hypoxia-ischemia on the nitric oxide synthase (NOS) cofactor tetrahydrobiopterin (BH4) and changes in the enzyme dimer state have not previously been studied. Cell-based studies have demonstrated the regulation of nitric oxide (NO) synthesis by intracellular BH4 levels. Activation of NOS requires two NOS polypeptides to form a homodimer. Dimerization results in the creation of high-affinity binding sites for BH4 and L-arginine. Our previous studies have indicated that nNOS activity falls 2 h post-hypoxia-ischemia in the immature rodent model. Thus, the objective of this study was to determine whether changes in nNOS dimeric state could be responsible for the decrease in nNOS activity. Using the immature rat model of HI in conjunction with LT-PAGE and Western blot analysis, we determined the effect of HI on NOS dimer state in hippocampus and cortex and the effects of pharmacologic modulation of NO levels during HI on dimer formation. Using high-performance liquid chromatography (HPLC) and electrospray tandem mass spectrometry (MS-MS), we measured BH4 and L-arginine levels respectively after HI under the same conditions. We found minimal or no changes in either BH4 levels or NOS dimer state at 2 h, 24 h and 7 day recovery from HI on postnatal day 7. In contrast, L-arginine levels were transiently increased in the hypoxic ischemic hemisphere. Thus, our data suggest that the previously described decrease in NOS activity after HI is not associated with depletion of the cofactor BH4, L-arginine substrate or changes in the NOS enzyme dimer state.