The Gothic church of the Holy Cross with a characteristic, single-pillar construction is one of the most interesting and, at the same time, oldest buildings of Kraków. It is localised in the town centre, neighbouring the Planty, i.e., the park founded on the place of old city fortifications. The church was built in two stages. The first structure, representing probably the Romanesque style, was erected around the turn of 11th century. It was followed by a Gothic church, whose constructing started from the eastern side of the chancel not later than in the early years of the 14th century. The stone used in the Holy Cross Church proves that in the Gothic times it was not only one of the essential building, but also decorative materials. Two main rock types: the finedetrital, Jurassic limestone with cherts from the Kraków region and the Istebna sandstone from a vicinity of Dobczyce were used for constructing purposes, while the fine-detrital Tertiary limestone from the Pińczów area was the material of minor significance. The northern and eastern walls of the chancel were erected of the broken stones. Stone elements are also present in plinths, wall pillars and window frames. The pillar supporting the palm vault of the nave is made of the Jurassic limestone and a medium-grained sandstone, while the Gothic ribs and the vault itself of the Tertiary limestone. Other rock types play the decorative role. The Dębnik limestone is seen in epitaph tablets and – in combination with the Sławniowice marble – in the church floor. The stones, both occurring outside and inside the church, show the signs of deterioration in the form of soiling, colour changes, efflorescences and chippings. Their intensity differs and depends on various factors. The most pronounced and dominating alterations that belong to the group no. II of stone deteriorations (i.e., colour changes / surface accumulations) affect the material used outside. The stone elements inside the church, thus unexposed to external factors, show lesser alterations. These changes belong mainly to the group no. I of deterioration (i.e., pit losses), being frequent in places but of low depth. The assessment of stone preservation is of particular importance in selecting proper methods of conservation that are focused on restoring the former appearance of stone elements of the church. For this reason, the authors described in details and classified into respective groups of changes all types of stone deterioration identified in the rocks used outside and inside the church. A geological report of this kind may help specialists establish a program of church conservation in the future. Identification of the most probable place of quarrying the rocks involved will also help in substituting damaged stone elements with new ones, if such an action is required.