Introduction: Subclinical deficiencies influence concentrations of related analytes and their gender differences. In this study, influence of common subclinical deficiencies on the correlations of parathyroid hormone with bone markers and their related analytes were evaluated. Methods: Participants aged 18 to 25 years from rural, central Kerala, who were clinically examined and found to be healthy took part in this observational cross sectional study. They were further evaluated by quantitative biochemical analytes with cut off levels fixed to exclude common subclinical diseases states and deficiencies. Results: Exclusion of clinical and subclinical disease states reduced sample number from about 600 to 142. There were more males excluded than females. Exclusion of all common deficiencies further reduced sample number from 142 to 40, during which the reduction in the number of females was much more marked than males. In the male sample, before exclusion of deficiencies, there were number of bone markers and related analytes correlating with PTH. But after exclusion of all deficiencies in the male sample, PTH positively correlated with osteocalcin and negatively correlated with bone alkaline phosphatase (Table 4), indicating that when PTH was increased, bone resorption and turnover were higher, and bone formation was low. In the female sample, even osteocalcin which was positively correlating with PTH before exclusion of deficiencies lost its correlation after exclusion. Conclusion: Exclusion of deficiencies related to parathyroid hormone brought out the gender differences in the correlations of PTH with bone markers and related analytes, indicating gender differences in the metabolism of bone.