Mullite samples doped with cobalt were derived from diphasic gels with constant atomic ratio (Al + Co)/Si = 3:1, where 0, 1, 2, and 3 at% of aluminum was replaced by cobalt. X-ray powder diffraction showed that the samples contained mullite phase and some amount of α-Al2O3 (for pure and doped samples) and CoAl2O4 (for doped samples). Cobalt doping caused an increase in unit-cell parameters of the mullite phase. Transmission electron microscopy and energy dispersive X-ray spectroscopy were used for sample microanalysis and determination of the chemical composition of the Co-doped mullite phase. The Rietveld method was performed for quantitative phase analysis of the samples and for structure refinement of the mullite phase in the samples. It was found that a small amount of Co2+, 0.36 wt%, substituted for Al3+ in the AlO6 octahedra of the mullite structure. Simultaneously, the same amount of tetrahedral Al3+ ions was likely substituted by Si4+ in the (Al,Si)O4 tetrahedra for the purpose of charge compensation. The remaining cobalt reacted with alumina forming CoAl2O4, and dissolved in the glassy phase. The proposed formula for Co-doped mullite is CoyAl4+2x–2ySi2–2x+yO10–x.