Naphthalene causes severe dose- and site-selective injury to mouse nonciliated bronchiolar (Clara) epithelial cells. Toxicity is characterized by exfoliation of injured Clara cells into the airway lumen 24 h after exposure. The purpose of this study was to define the temporal pattern of intracellular changes immediately following naphthalene treatment, with the goal of identifying critical early events involved in cytotoxicity. Mice were injected with naphthalene or carrier and were killed 1, 2, 3, and 6 h after treatment (PT). Loss of membrane integrity was assessed by ethidium homodimer-1 permeability and confocal microscopy. Cell morphology and ultrastructure were evaluated using high-resolution light and electron microscopy. Permeable cells were found only in terminal bronchioles and increased in abundance with time PT. At 2 and 3 h PT, when most Clara cells had early signs of injury, few permeable cells were detected. Many Clara cells had apical membrane blebs that contained abundant, swollen, smooth endoplasmic reticulum (SER) and few other organelles. By 6 h PT many Clara cells were membrane-permeable. However, many permeable Clara cells lacked apical blebs and SER was less abundant in these cells. Cytoplasmic blebbing may be a mechanism to protect the cell by isolating and removing damaged SER. We conclude that the early stages of injury include SER swelling and bleb formation which precede increases in cell membrane permeability after acute naphthalene injury to bronchiolar Clara cells in vivo.