Feedstock and compost samples were collected from twenty composting plants and analysed from the microbiological point of view. Faecal indicator organisms were determined in order to evaluate the efficacy of processes for the removal of pathogenic micro-organisms with similar survival characteristics and to verify their suitability as appropriate markers of microbial quality of composted products. In addition to the classical bacterial indicators, selected organisms, such as Salmonella, Giardia, Cryptosporidium, Clostridium spores and helminth ova, were investigated. Statistically significant differences in the removal of the different micro-organisms were observed with regard to both the different composting plants (P < 0.05) and feedstock composition (P < 0.05). In fact, compost obtained by feedstock containing sewage sludge was shown to have a better hygienic quality in comparison with compost containing green discards and municipal solid waste as raw matter. Giardia cysts, Cryptosporidium oocysts and helminth ova were not effective indicators of hygienic quality of compost, whereas Clostridium perfringens spores, because of their high resistance to treatments, could be considered as an additional model for assessing the composting process, especially with regard to more resistant pathogen reduction.