Brush border hydrolases of the differentiated intestinal cell line Caco-2 are transported to the microvillar membrane at different rates. This asynchronism is due to at least two rate-limiting events, a pre- and an intra-Golgi step. The retardation of sucrase-isomaltase, a slowly migrating hydrolase, versus dipeptidylpeptidase IV, a rapidly transported enzyme, is neither due to differential trimming of N-linked carbohydrates nor due to oligomerization. In this study, the conformational maturation of biosynthetically labeled sucrase-isomaltase and dipeptidylpeptidase IV was probed by conformation-specific antibodies and proteases. These assays enabled us to correlate the conformational maturation of the two enzymes with their rates of transport. Furthermore, two naturally occurring mutants of sucrase-isomaltase with impaired intracellular transport displayed an immature conformation. It is proposed that differential kinetics of folding might be the underlying cause for both the pre- and the intra-Golgi steps of asynchronous intracellular transport. Furthermore, a proper tertiary structure might be a prerequisite for sucrase-isomaltase to leave the Golgi apparatus.