Rheumatoid Arthritis (RA) is an autoimmune disorder that results in inflamed joints and osteoporosis. Previous studies have shown that Mycobacterium avium subspecies Paratuberculosis (MAP) has a role in the downregulation of active osteocalcin in Crohn’s disease (CD). Since RA and CD have a similar pathology, we hypothesize that active inflammation following MAP infection will result in downregulation of active osteocalcin in RA patients. In this study, a total of 82 individuals (48 RA and 34 healthy) were examined for MAP status and for active osteocalcin. Out of the 48 RA patients, 18 were MAP positive compared to only 1 out of 34 healthy control (P-values < 0.05). Overall, active osteocalcin levels between RA (2.70 ± 0.87 ng/mL) were significantly lower than healthy controls (5.84 ± 1.42 ng/mL, P-values < 0.05). MAP positive RA patients active osteocalcin levels were lower (0.60 ± 0.31 ng/mL) than MAP negative RA patients (3.85 ± 1.31 ng/mL). The active osteocalcin level in healthy MAP positive controls were lower (1.65 ng/mL) than healthy MAP negative controls (5.96 ± 1.45 ng/mL). The level of active osteocalcin in all MAP positive patients was significantly lower (0.66 ± 0.29 ng/mL) than all MAP negative patients (4.95 ± 0.98 ng/mL, P-values < 0.05). The correlation between presence of MAP in RA individuals and downregulation of active osteocalcin supports a role of MAP as a pathogenic element in RA. In addition, we tested three Single Nucleotide Polymorphisms (SNPs) in TNFα, TNFRSF1A and TNFRSF1B by TaqMan genotyping from peripheral blood samples of the 82 subjects. These SNPs were used to determine whether they influence the levels of osteocalcin in RA and healthy patients. Patients with the SNP TNFRSF1B:rs3397 who had TT genotype had a significantly lower osteocalcin level compared with patients without SNP who had CC genotype (0.98 ± 0.35 ng/mL vs. 1.86 ± 0.61 ng/mL). Overall, there was a correlation of the presence of these SNPs and the downregulation of osteocalcin in RA.