Endomorphins are endogenous peptides that have high affinity and selectivity for the mu-opiate receptor and potent analgesic activity. The distributions of endomorphin 1 (Tyr-Pro-Trp-Phe-NH2; EM1) and endomorphin 2 (Tyr-Pro-Phe-Phe-NH2; EM2) in the rat central nervous system were determined by immunocytochemistry with two antisera, each demonstrating clear preference for the target antigen. Perikarya expressing EM2-like immunoreactivity were present in the posterior hypothalamus, whereas those expressing EM1-like immunoreactivity were present in both the posterior hypothalamus and the nucleus of the solitary tract (NTS). EM1-like immunoreactivity was more widely and densely distributed throughout the brain than was EM2-like immunoreactivity, whereas EM2-like immunoreactivity was more prevalent in the spinal cord than was EM1-like immunoreactivity. The greatest density of EM1-like-immunoreactive fibers was detected in the parabrachial nucleus and the NTS, with notable staining in the septum, diagonal band, bed nucleus of the stria terminalis, organum vasculosum, nucleus of Meynert, paraventricular thalamic nucleus, posterior hypothalamic nucleus, periaqueductal gray, locus coeruleus, nucleus accumbens, and amygdala. The greatest density of EM2-like-immunoreactive fibers was detected in the superficial laminae of the spinal cord dorsal horn and the nucleus of the spinal trigeminal tract. The overall pattern of immunoreactivities was similar in rat, mouse, and guinea pig, but some differences were observed. In many but not in all locations, immunoreactive fibers were prominently present in regions in which mu receptors are reported to be concentrated. The neuroanatomical results suggest that endomorphins participate in modulating nociceptive and autonomic nervous system processes and responsiveness to stress.