To identify the early renal lesions in cystinosis, including whether the "swan neck" deformity of the proximal tubule is a congenital or an acquired lesion, we performed renal function tests and kidney biopsies on two cystinotic infants, on one at 5 and 14 months and on the other at 6 and 12 months of age. The "swan neck" deformity appears to be an acquired lesion for two reasons. First, the characteristic thin neck of the proximal tubule was not demonstrated by nephron microdissection or light microscopy until after 6 months of life. Second, electron microscopy revealed that prior to the development of the lesion, the tubular cells in the neck region of the proximal tubule were undergoing degenerative changes. Renal function tests indicated that the manifestations of the Fanconi syndrome correlated with the stages of development of the "swan neck" lesion. Minute crystalline spaces having some of the characteristics of lysosomal cystine crystals appeared in the early biopsies only in that portion of the proximal tubule which was undergoing atrophy to form the "swan neck" lesion observed in the later biopsies. These findings provide evidence of at least a temporal relationship between apparent cellular cystine accumulation and the development of the "swan neck" lesion and the Fanconi syndrome.