Background: Kidney stones is one of the many causes of chronic kidney disease (CKD) in clinical and kidney fibrosis in histopathology presentation. Its occurs characterized by the presence of glomerulosclerosis (GS), tubulointerstitial fibrosis (TIF) and tubular atrophy (TA). This research aims to find out that the effect of glomerulosclerosis index (GSI), tubular index (TI), and matrix metalloprotein (MMP-9) against serum creatinine (SC) and estimated glomerular filtration rate (eGFR) Â in kidney stone disease. Â Methode: A total of 62 samples of kidney biopsy patients during kidney stone surgery in Sanglah General Hospital Denpasar-Bali, from February until December 2013. Kidney tissue biopsy stained with Masson's Trichrome.Â Determination of GSI was counted GS in 30 glomerular in power field 400, and TI was counted normal tubular in 30 glomerular in power field 400, and MMP-9 was carried out using Kit Methode. Structural Equation Modelling (SEM) program Analysis of Moment Structure (AMOS) was used to analyze the effect of GSI, TI, and MMP-9 against SC and eGFR in kidney stone patients. Â Results: Descriptive analysis were male 43 (69.35%), and female 19 (30.65%). Age (years) 50.0 Â± 10.56; SC (mg/dl) 1.71 (0.47 to 6.76); GSI (glomerosclerosis/30 glomerular) 11 (0-30); TI (normal tubulars/30 glomerular) 850.24 (118 to1523); eGFR (ml/min) 65.41 Â± 20.47; Leukocytes (cells/mm3) 7.82 Â± 1.89; and MMP-9 (ng/ml) 6.13 (0.05 to 28.37). Direct and total effect (direct and indirect effect) were GS to eGFR = -0.16 and 0.33; TI to eLFG = 0.28 and 0.36, GS to SC = 0.31; TI to SC = -0.14; MMP-9 to SC = -0.16; SC to eGFR = -0.55. Conclusion:Â Direct and total effect of GSI to eGFR were negative (-) 16% and (-) 33%; TI to eGFR were positive (+) 28% and (+) 36%. Direct effect (without indirect effect; direct effect as same as a total effect) of GSI, MMP-9, and TI to SC were positive (+) 31%, negative (-) 16%; and negative (-) 14% consecutively. Direct effect or total effect of SC to eGFR were negative (-) 55%. The results concluded that the effect measurements of urinary MMP-9, and GSI, and TI score to SC were negative (-) 16 %, positive (+) 31 % and negative (-) 14 % consecutively. The effect measurements of urinary MMP-9, and GSI, and TI score to eGFR were negative (-) 0.09 %, negative (-) 16 %, and positive (+) 28 %.