Nephropathic cystinosis is rare genetic disease characterized by defective lysosomal cystine transport and increased lysosomal cystine. Corneal Cystine Crystal Scoring (CCCS) for diagnosis of nephropathic cystinosis was studied in all suspected children with renal Fanconi syndrome and siblings of diagnosed cases over a two year period. In addition to oral cysteamine, cysteamine eye drops were provided to all diagnosed patients and CCCS was followed up on a quarterly basis. Of 33 screened cases, 14 had corneal cystine crystals. Crystals were absent in two cystinotic patients under the age of 20 months. The mean age at diagnosis was 52.7 months and five patients had ERSD. After six months of treatment, the mean CCCS did not increase from the initial value of 1.81; associated with a decrease of 0.5 in two cases and a similar increase in two others. Scores decreased in two other patients after 12 months. Compliance was generally inadequate due to the high frequency of administration and the need for multi-drug regimen. CCCS is a simple and reasonably sensitive method for diagnosis of nephropathic cystinosis above two years of age. Topical treatment with cysteamine eye drops prevents progression of deposits and may decrease it with adequate compliance. Further follow up is still recommended to monitor long term effects of both systemic and topical cysteamine therapy.