The sunshine vitamin is in the limelight for the last couple of years. Though Pakistan is located at favorable latitude and longitude yet vast majority of its people suffer from vitamin D deficiency. Calcium homeostasis, bone metabolism and many other functions of body are influenced by vitamin D. Nuclear vitamin D receptor and group specific vitamin D binding proteins are two important proteins play role in vitamin D metabolism and encoded by VDR and GC genes. There could be many reasons but in this study six single nucleotide polymorphisms in GC, VDR and CYP2R1 genes were looked into for their possible association with vitamin D deficiency. Blood samples of four hundred subjects were collected. Vitamin D and parathyroid harmone levels were calculated by chemiluminescence method. DNA extraction was carried out by phenolchloroform method. The qualitative and quantitative analysis of DNA was carried out on agarose gel electrophoresis. Tetra amplification refractory mutation system polymerase chain reaction was performed to genotype rs7041, rs4588, rs2060793, rs2282679, rs3847987, and rs7974353. Genotypic and allelic frequencies with relative risk was calculated. In Silico protein modelling, docking and analysis of rs7041 was done. Overall 77.5% subjects were found to be with vitamin D deficiency/insufficiency. There were 35% from newborn to 20 years age group, 88.8% from 21-40 years and 95.8% from to 41-60 years.Significant negative correlation was observed between vitamin D and parathyroid hormone levels. rs 7041 belonging to GC genes showed T>G polymorphism. Major allele was T and minor allele was G. Minor allele “G” with genotype GG could be a risk allele contributing in vitamin D deficiency. rs7974353 belonging to VDR gene showed T>A polymorphism. Though “TT’ was in high frequency in VDD subjects compared to control yet insignificant association with VDD was noted. RR for both alleles and genotypes TA and AA was not significant with reference to homozygous wild type TT (0.6 for AT, 0.7 for AA). Results might had been xxi sigificant if thenumber of subjects were more. Rest of the four SNPs showed equal frequency in control and cases and hence showed no association with vitamin D deficiency. In silico model of SNP rs 7041 showed variation in the 3D structure of protein because of replacement of asparctic acid by glutamic acid. This can explain the cause of VDD / VDI due to poor docking of vitamin D with its binding protein. Conclusion is that rs7041 and possibly rs7974353 are contributing to VDD / VDI in studied group. Results are supported by In silico analysis of rs 7041.