Axonal swellings, characterized by focal accumulations of membranous organelles at presumed sites of interrupted axonal transport, occur in diffuse axonal injury (DAI) in human, blunt head injury and in animal models of nondisruptive axonal injury. Membranous organelles are transported by fast axonal transport in association with microtubules. Although loss of microtubules has been documented at levels of injury severe enough to result in permeabilization of the axolemma to tracers such as horseradish peroxidase, there has been no detailed analysis of responses by microtubules in less severe or milder forms of nondisruptive axonal injury. To test the hypothesis that in less severe forms of axonal injury there is a rapid response by axonal microtubules that might provide an explanation for loss of fast axonal transport, we have carried out a morphometric analysis of microtubules in CNS axons after stretch-injury. There is loss of microtubules at nodes of Ranvier with nodal blebs within 15 min of injury, and in internodal axonal swellings between 2 and 4 h. There is a return to control values at nodes of Ranvier by 4 h, and at the internode by 24 h. There is no loss of microtubules at paranodes, although there is a reduction in their density in the first 2 h after injury. The greatest loss of microtubules occurs at sites of axolemma infolding. Hypothetical mechanisms that might lead to this loss resulting in focal disruption of fast axonal transport and the formation of axonal swellings are discussed.