Neuropeptides have important roles in modulating behavioral patterns such as social interaction. With the aim to determine the presence of neuropeptides known to be involved in social interaction as well as novel peptides, we used MALDI-TOF/MS to analyze neuropeptide profiles in some medaka brain regions. In the telencephalon, hypothalamus, and pituitary gland, 3, 6, and 10 peaks, respectively, were identified as neuropeptides (Arg-vasotocin [AVT], growth hormone-releasing hormone [GHRH], neuropeptide FF, substance P [SP], somatostatin-1 and -2, melanin-concentrating hormone [MCH], MCH gene-related peptide [Mgrp], melanocyte-stimulating hormone [MSH], corticotropin-like intermediate lobe peptide [CLIP], and beta-endorphin). The neuropeptide profile of telencephalon similar to that of the hypothalamus, but completely different from that of pituitary gland. For the future genetic analysis, we identified cDNAs encoding precursor proteins for the identified peptides. We also detect its expression of gamma-prepro-tachykinin gene encoding a SP precursor protein in both the telencephalon and hypothalamus. Our results indicated that the medaka brain contains some neuropeptides (AVT, SP, and somatostatins) that may be involved in modulating medaka behaviors such as social interaction.