The objective of this study was to determine the concentration of introduced proteins in the fiber fractions of transgenic cotton (Gossypium hirsutum L.) before and after processing. Two novel cotton varieties were developed by genetic transformation technology. One variety expressed the CryIA(c) insecticidal protein derived from Bacillus thuringiensis var. kurstaki. The second cotton variety expressed the CP4 EPSPS (5-enolpyruvyl shikimate-3-phosphate synthase) protein, originally found in Agrobacterium sp., which confers tolerance to glyphosate herbicide. Levels of the CryIA(c) and CP4 EPSPS proteins in raw lint, combed lint, raw linters, and processed linter brown stock from these cotton varieties were analyzed by means of western blot, insect bioassay [for CryIA(c) protein only], or both. The CryIA(c) protein was present in raw linters (0.17 μg g -1 ), but it was not detected in either raw or combed lint. The CP4 EPSPS protein was detected at low levels (<0.5 pg g -1 ) in combed lint, but not in processed linter brown stock. Inactivation of the CryIA(c) and CP4 EPSPS proteins in the first processing step for linters indicates that these proteins will not be present in cotton linter products. Similarly, the typical heat and chemical processing of cotton lint should also denature any transgenic protein(s) present.