Cathodoluminescence (CL) microscopy studies were performed to unravel internal structures and zonations of carbonates from 6 unaltered hypabyssal kimberlites from several Mesozoic - Paleozoic kimberlite pipes of the Siberian craton. Different generations of prograde and retrograde carbonate grains/domains were identified. Most investigated kimberlite samples are unusually fresh and contain abundant unaltered olivine. Only minor amounts of carbonates of a primary magmatic origin were found; most carbonates are of secondary origin formed during late metasomatic or hydrothermal events. A rare carbonatite xenolith discovered in the Malokuonapskaya kimberlite contains abundant apatite and monazite; an apatite inclusion was detected in one zircon grain. Some apatites contain oriented lamellae of monazite. Early studies of the carbonate minerals in this xenolith demonstrated a trace amount of Sr; all these characteristics are typical of carbonatite. We conclude that carbonate minerals play a significant role in the evolution of hypabyssal kimberlites of the Siberian craton. The CL-studies of these minerals provide significant insights into their growth history and help to differentiate different parageneses, as either primary or secondary. Carbonatite xenoliths are of vital significance for the discussion of a possible genetic interrelation of kimberlite and carbonatite melts in the mantle. The present results may serve as a starting point for future studies of these carbonate minerals, using electron-microprobe, micro-PIXE or other high-resolution techniques. Future in-situ oxygen and carbon isotope analyses, as well as inclusions of melt, fluid, and minerals in different carbonate domains, will add essential new data with which to further unravel the genesis of the kimberlite-carbonatite association.