Recent reports have indicated that analysis of changes in the staining characteristics of gonadotropin-releasing hormone (GnRH) neurons and characterization of morphological plasticity of the related structural framework may help to elucidate the physiological mechanisms involved in neuroendocrine control of mammalian reproduction. Whether comparative studies will facilitate this process or simply elucidate species-specific mechanisms is not yet clear. The present study was performed in order to begin analysis of GnRH neurons in a seasonally breeding species that exhibits an unusually long ovulatory luteinizing hormone (LH) surge. To this end, light microscopy and image analysis were used to characterize distribution and morphology of GnRH neurons in 15 adult male and female ponies. Samples were collected in the middle of the normal ovulatory season. Unipolar, bipolar, and multipolar GnRH neurons were organized in a loosely defined continuum that extended from the medial septum to tuberoinfundibular areas in the medical basal hypothalamus (MBH). Most cells were bipolar, and the majority of neurons were located in the MBH. Fiber projections to the median eminence included presumptive pathways similar to those previously described in other species. Image analysis of cell size indicated that cells in the MBH were larger than those in preoptic areas and GnRH neurons in both of these locations were larger than neurons in rostral areas of the medial septum. Results from this experiment suggest that the large population of MBH GnRH neurons in the equine species is likely to be of primary importance to reproductive function, whereas cells in other areas are fewer and smaller. Further work is needed to characterize morphological characteristics that may be related to physiological fluctuations in reproductive function of the equine species.