Background: The etiology of intellectual disability (ID) can be genetics or environmental including neurological disorders, gastrointestinal disorders and behavioral/psychiatric problems. Therefore, current study was aimed to diagnose possible health disparities by collective results of clinical manifestations, urinary biochemical and chromosomal analysis. Materials and methods: The clinical manifestations were studied for all 34 ID affected children from Gujarat. The results obtained from biochemical and chromosomal investigations were recorded and values were calculated and compared with all clinical data sets to point out significant findings. Results: Urine analysis revealed the presence of abnormal concentration of glucose, ketones, nitrites, bilirubin and urobilinogen in different groups of children with ID. The results from specific gravity test revealed hydration and dehydration status of individuals. Giemsa banding (G-banding) analysis confirmed the suspected Down syndrome (trisomy 21) in 5 children and no other chromosomal anomalies were detected from remaining samples. Conclusion: Microcephaly, macrocephaly, seizure, speech abnormality, short stature, oral cavity defect and facial dysmorphia were more frequently observed in Down syndrome (DS) children as compared to unclassified intellectually disabled (ID). Comparatively more number of DS children showed urinary glucose, ketone and nitrite excretion than ID. Bilirubin, blood and urobilinogen were more frequently excreted in ID children.