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Cystinosis is a rare autosomal recessive lysosomal storage disease with high morbidity and mortality. It is caused by mutations in the CTNS gene that encodes the cystine transporter, cystinosin, which leads to lysosomal cystine accumulation. It is the major cause of inherited Fanconi syndrome and should be suspected in young children with failure to thrive and signs of renal proximal tubular damage. The diagnosis can be missed in infants, because not all signs of renal Fanconi syndrome are present during the first months of life. Elevated white blood cell cystine content is the corner stone for the diagnosis. Since chitotriosidase (CHIT1 or chitinase-1) is mainly produced by activated macrophages both in normal and inflammatory conditions. Which suggests that cystinosis should be included in the differential diagnosis of disorders with increased plasma chitotriosidase activity. This study is aimed to investigate the impact of cystinosis on the renal function in relation to age at detection and initiation of treatment course,besides estimating serum chitotriosidase level,as a screening marker and therapeutic monitor for cystinosis disease in Iraqi children with cystinosis. The present study is a case-control study included a samples of 30 children with nephropathic cystinosis, compared to 25 healthy control children from those attending at The Genetic Rare Diseases Center/AL- Emamain AL-Kadhimain teaching hospital, Baghdad-Iraq. Our results report patients who started taking the medication (cysteamine) before two years of age were presented with significantly lower levels of cystine and chitotriosidase in addition to better renal function (higher GFR) (P-value = 0.0001) .In other words, earlier treatment led to better disease control and less deterioration of renal function. In conclusion serum chitotriosidase activity estimation might aid in monitoring therapeutic benefit of cysteamine therapy and the prognosis of the disease when WBC cystine assessment is not available. [ABSTRACT FROM AUTHOR]