The sulfur compounds of refractory organic substances (ROS) of different origin have been characterized. Total organic sulfur was determined by elemental analysis. Sulfur-containing amino acids methionine and cystine were analyzed chromatographically after hydrolysis with HCl or by proteolytic digestion using enzymes. The results obtained from elemental analysis show that the total amount of sulfur is strongly dependent on the origin of the samples, because of different environmental factors during the formation of ROS. For naturally occurring samples isolated from soil seepage water, bog lake water and ground water the carbon-to-sulfur atomic ratios (C/S) decrease with the stage of humification, because of preferential loss of carbon. In humic acids (HA) isolated from secondary effluent the high value of the nitrogen-to-sulfur ratio (N/S) was indicative of a large amount of protein-derived nitrogen and sulfur compounds. In the solutions from acid hydrolysis the total amount of amino acid carbon related to the dissolved organic carbon (DOC) was generally less than 5%. Percentages of cystine related to all the amino acids detected were in the range 4 to 16%; methionine was below the detection limit for most samples. The results show that cystine is very important among the amino acids released. Enzymatic release generally resulted in smaller amounts of amino acids, indicating that these molecules are not only present in bioavailable protein-like structures. The data were compared with those from other approaches reported in the literature for the speciation of sulfur forms in ROS, including potentiometric titration, differential reduction methods, and spectroscopic investigations.