We performed in vivo diffusion tensor imaging (DTI) in a total of 33 patients with brain tuberculomas (BT). Thirteen of them had surgical excision of the lesion as it was clinically indicated, and in these samples matrix metalloproteinase-9 (MMP-9) expression was quantified. We correlated the results of DTI indices like fractional anisotropy (FA), mean diffusivity (MD), linear anisotropy (CL), planar anisotropy (CP) and spherical anisotropy (CS) with MMP-9 expression. In addition, the remaining 20 patients had serial DTI studies while on specific anti-tuberculous drug therapy and DTI indices in these patients were quantified. The FA, CL and CP significantly decreased while MD and CS significantly increased in BT compared to normal white matter. The FA, CL and CP showed negative correlation with MMP-9 while CS correlated positively. In serial follow-up studies in 20 patients FA, CL and CP showed significant increase while CS decreased significantly over time. We conclude that DTI indices show strong correlation with MMP-9 and these may be used as a surrogate marker of MMP-9 expression in BT. In addition, these indices may be of value in assessing the therapeutic response in patients with BT who are treated only with specific anti-tuberculous drugs.