Nencki's main scientific interest concentrated on urea synthesis, the chemistry of purines and biological oxidation of aromatic compounds. He was also interested in the structure of proteins, enzymatic processes in the intestine and bacterial biochemistry. One of his achievements was for example demonstration that urea is formed in the organism from amino acids rather than being preformed on a protein molecule and that it is accompanied by binding of carbon dioxide.
Among Nencki's greatest achievements was his study on the chemical structure of haemoglobin. He identified haemopyrrole among degradation products of haemoglobin and showed its identity with one of the products obtained by Leon Marchlewski from chlorophyll.
He was the first to rigorously analyze the cause of smell in urine following eating asparagus, which he attributed to methanethiol. He made Phenyl salicylate or salol in 1886, and introduced it as a mild intestinal antiseptic (which it is not) . The "salol principle" (or "nencki principle" or "salol nencki principle" ...) is used to design drugs .
- Nencki, Marceli (1891). "Ueber das vorkommen von methylmercaptan im menschlichen harn nach spargelgenuss". Arch Exp Path Pharmak 28: 206–209. doi:10.1007/BF01824333.