Infections related to modern surgical procedures present a difficult problem for contemporary medicine. Infections acquired during surgery represent a risk factor related to therapeutical interventions. Eradication of microorganisms from hospital operating theatre environment may contribute to reduction of infections as the laminar flow air-conditioning considerably reduces the number of microorganisms in the hospital environment. The objective of the study was to evaluate the occurrence of fungi in air-conditioned operating theatre rooms. The study was carried out in one of the hospitals in Krak6w during December 2009. Indoor air samples and imprints from the walls were collected from five operating theatre rooms. A total of fifty indoor air samples were collected with a MAS-100 device, and twenty five imprints from the walls were collected using a Count Tact method. Fungal growth was observed in 48 air samples; the average numbers of fungi were within the range of 5-100 c.f.u. in one cubic metre of the air. Fungi were detected only in four samples of the wall imprints; the number of fungi was 0.01 c.f.u. per one square centimetre of the surface. The mould genus Aspergillus was most frequently isolated, and the species A. fumigatus and A. versicolor were the dominating ones. To ensure microbiological cleanness of hospital operating theatre, the air-conditioning system should be properly maintained. Domination of the Aspergillus fungi in indoor air as well as increase in the number of moulds in the samples taken in evenings (p < 0.05) may suggest that the room decontamination procedures were neglected.