Agrin is a high-molecular weight extracellular matrix molecule, initially purified from the electric organ of the marine ray Torpedo californica, which induces on the surface of cultured myotubes the formation of postsynaptic specializations similar to those found at the neuromuscular junction. Agrin immunoreactivity is highly concentrated in the basal lamina of the synaptic cleft but is also found in a number of other tissues where its function is not known. We characterized agrin associated with two basal laminae from the central nervous system, the inner limiting membrane of the retina and the mesencephalic external limiting membrane. A major broad band with an apparent molecular weight of > 300 kDa was identified in immunoblots of isolated basal laminae from retina, mesencephalon, kidney and muscle, showing that basal lamina-bound agrin from the central nervous system and that from non-neural tissues have similar molecular sizes. Agrin is stably but not covalently bound to the inner limiting membrane and could be completely removed only with strong detergents. Agrin could be partially extracted with buffers that are also able to partially release acetylcholine receptor aggregation activity from the neuromuscular junction or from the electric organ. Despite these immunological and biochemical similarities, agrin from both central nervous system-derived basal laminae was not able to induce acetylcholine receptor aggregation on cultured myotubes. This shows that functionally different agrin isoforms are associated with basal laminae in the central nervous system compared to the neuromuscular junction or the electric organ.