The present study deals with the application of High Resolution Transmission Electron Microscopy (HRTEM) to dark layers, occurring in the speleothems of Domica Cave (Slovakia). Chemical pre-treatment was necessary for sample purification and the effective extraction of carbon soot. For purposes of comparison, soot aggregates obtained from laboratory experiments on the combustion of beech wood and collected from a diesel engine also were studied. HRTEM analyses of combustion products permit a distinction to be made between soot aggregates that originated in different combustion processes. The diameter of spherical, primary particles depends on the conditions of combustion, notably temperature. Burning in diesel engines produces soot with relatively small, primary particles (diameter d p = 34 ± 4 nm). Primary, spherical particles of soot aggregates, obtained from the combustion of beech wood, were larger (diameter d p = 42 ± 5 nm). The diameters of primary particles of soot separated from Domica flowstones (samples DOM1 and DOM2) were similar to the wood samples (d p = 50 ± 9 nm). Another type of carbonaceous particle, obtained in the combustion process, had a spherical shape, but the diameter of about 50–500 nm was significantly larger than that of soot. Analyses performed on two samples (DOM S1 and DOM S2) confirmed that the black laminae owed their colour to particles, formed during wood combustion and later retained in the speleothems.