The recovery of three stone-like ovoid objects within the burial of a pre-Mesolithic (Late Pleistocene/Early Holocene) individual at Al Khiday cemetery (Central Sudan) raises the question of the nature and origin of these objects. The position in which the objects were found in relation to the human skeleton suggested a pathological condition affecting the individual, possibly urinary bladder, kidney stones or gallstones. To solve this issue, a multi-analytical approach, consisting of tomographic, microstructural and compositional analyses, was therefore performed. Based on their microstructure and mineralogical composition, consisting of hydroxylapatite and whitlockite, the investigated stones were identified as primary (endogenous) prostatic calculi. In addition, the occurrence of bacterial imprints also indicates on-going infectious processes in the individual. This discovery of the earliest known case of lithiasis extends the appearance of prostatic stones into the Late Pleistocene/Early Holocene, a disease which therefore can no longer be considered exclusive to the modern era, but which also affected prehistoric individuals, whose lifestyle and diet were significantly different to our own.