The electronic and magnetic structures of Mn-doped 6H-SiC have been investigated using ab initio calculations. Various configurations of Mn sites and vacancy types have been considered. The calculations showed that a substitutional Mn atom at either Si or C sites possesses a magnetic moment. The Mn atom at Si site possesses larger magnetic moment than Mn atom at C site. The magnetic properties of ferromagnetically and antiferromagnetically coupled pair of Mn atoms in the presence of vacancies have also been explored. Our calculations show that antiferromagnetically coupled pair of Mn atoms at Si sites with neighboring C vacancy is magnetically more stable. Relaxation effects were also studied. The results are correlated to the measured magnetic properties obtained for Mn-implanted 6H-SiC for various Mn concentrations. (C) 2012 American Institute of Physics.