Background: Urinary stone disease (USD) is among the ancient human known diseases that could be often complicated by pain and severe complications and numerous predisposing factors play a key role in initiation and development of stones. Objectives of Research: The present research examined several biological and clinical determinants that play a role in urinary stone disease (USD), with identifying the stone chemical composition, determining any corresponding bacterial infections, and molecular evaluating of some genetic predispositions of the (USD) patients. Methods and Materials: The current study was able to obtain samples of Hundred Stones, Blood, and Urine of (USD) patients in the AL-Hussein Educational Hospital and Safeer AL- Hussein Hospital in Karbala Province between October 2024 and March 2025; where these USD patients were aged between (18-79). Chemical compositions of kidney stones were analyzed using Biolabo- France kit, related bacterial infections were determined using ViteK test kit and Molecular analysis of the corresponding SNPs (rs1042636 of CaSR gene, rs219778 of CLDN14 gene, and rs10917002 of ALPL gene) in the present study was estimated using Allele Specific PCR and further DNA Sequencing was adopted to establish the relationship between stone types, bacterial infection and the genetic predisposing factors in (US). Results: Evaluating the prevalence of the kidney stones in (USD) patients greater prevalence was reported in the male (60%). And the chemical makeup showed the most Likely type of Stones were Calcium oxalate (40 percent), mixed Sat (31 percent) and last uric (27 percent). Only 33% of patients possessed the history of recurrences in the occurrence of stone formation, whereas diabetes and hypertension were observable in 31% and 23% of cases, respectively. Urine bacterial cultures showed that the majority of the stones (78 percent culture-negative) were of metabolic nature, whereas Klebsiella pneumoniae and Escherichia coli were more commonly noted in culture-positive ones and thus may have a contributory role in culture-related in-vivo urinary tract infection stones. Statistically, significant (p<0.001) relationship was determined between the type of bacteria and stone composition. Three (CaSR, CLDN14 and ALPL) of the key genes that were genotyped had a high prevalence of the AG genotype in CaSR (87%) and CLDN14 (97%). It was observed that a strong association (p<0.001), between the allele ALPL_C and certain types of stones, in particular calcium phosphate and mixed calcium-uric acid stones, was identified. DNA Sequencing of a small number of the PCR DNA products to analyze the Nitrogen bases of (rs1042636 of CaSR gene and rs219778 of CLDN14 gene) found perfect matches with already published sequences in NCBI Environment based on the Accession Numbers (ACCESSION PV871973) and (ACCESSION PV926278) respectively. This is in line with what the previous literature proposes that dysregulation of the production of ALPL which is a gene that participates in phosphate metabolism can predispose individuals to the occurrence of nephrolithiasis. Conclusions: the results confirm that the development of urinary stones is multifactorial, and it happens due to genetic variation, microbial effect, metabolic disorder, and demographic outcomes.