Gram-negative bacteria concentration in water effluent from a dental unit, and in dental aerosol forming during the work of a dental handpiece, was assessed. The study was conducted on 25 dental units before and after a 2-week period of using a disinfecntant for water in dental units waterlines (DUWL). The contamination of water with Gram-negative bacteria before disinfection was 18–398 × 10³ cfu/ml, and after disinfection, bacteria were not found. The concentration of Gram-negative bacteria in the air before disinfection was 0–23 × 10¹ cfu/m³, and after disinfection - 0–8 × 10¹ cfu/m³. Simultaneously, the water and air were sampled to determine bacterial endotoxin. The statistical analysis did not show correlation between endotoxin concentration and Gram-negative bacteria concentration for the water before disinfection, and for the air before and after disinfection of DUWL water. Because the number of bacteria in the water after disinfection dropped to zero, statistical methods could not be used. The performed analysis suggests that bacterial endotoxin concentration is not indicative of Gram-negative bacteria contamination. Thus, bacterial endotoxin determination is not recommended as a method of monitoring the microbiological quality of DUWL water and dental aerosols.