Conventional fractionation procedures were used in an effort to define the subcellular distribution of the Thy-1 alloantigen in whole mouse brain. After discontinuous sucrose density gradient centrifugation of isotonic postnuclear particulate fractions, the bulk of Thy-1 was recovered in regions of the gradients containing synaptosomes. The synaptosome fraction that banded at 1.2 M sucrose yielded a specific activity for Thy-1 significantly greater than the synaptosomes separating at 1.4 M sucrose. Osmotic lysis of both synaptosome fractions resulted in further enrichment in Thy-1 activity with no concomitant decrease in yields. The synaptosomal membranes obtained in this way were subsequently treated with Triton X-100 and subjected to further density gradient centrifugation. Although the detergent treatment resulted in some loss of antigenic activity, the gradient fractions that contained Thy-1 also were found by electron microscopy to be richest in synaptic junctional complexes. These findings suggest that Thy-1 is associated with synaptosomes and synaptic junctional complexes and therefore may be involved in the formation and/or maintenance of synaptic connections.