Vitamin D deficiency (VDD) has been reported from Pakistan in randomly selected healthy volunteers, patients and community females. In all studies a variable proportion (25.9%-31%) of the subjects had secondary hyperparathyroidism, as a compensatory response to VDD. However, a significant number of subjects with VDD show blunted Parathyroid hormone response. This phenomenon has been described in literature as functional hypoparathyroidism. we hypothesized that the presence of secondary hyperparathyroidism in our population could have been due to CaSR polymorphisms. In this cross-sectional study, we analyzed 140 pre-menopausal females with vitamin D deficiency for A986S and R990G CaSR gene polymorphisms. Patients bearing the GG genotype of R990G SNP had higher plasma Parathyroid hormone levels and lower serum calcium levels in comparison with the AG and AA genotype subjects. While Haplotypes G:G and G:T of the two polymorphisms were significantly associated with higher Parathyroid hormone and lower calcium levels respectively. These findings suggest that Measures to address secondary hyperparathyroidism and its associated long latency effects in our population are urgently needed