Analysis of arterial blood gases is necessary for managing the respiratory and metabolic parameters of patients in the intensive care unit. The aim of this study was to compare the effects of heparin 1000 and heparin 5000 units on arterial blood gases in patients admitted to the intensive care unit. This study was a triple-blinded clinical trial. A total of 78 patients with head injury were randomly selected from the emergency department of a hospital in an urban area of Iran in 2017. Data was collected using a questionnaire and a checklist of laboratory parameters. Data was analyzed using descriptive and inferential statistical methods via the R software. Statistically significant differences in Na, SaO2, Ca, BEecf (p < 0.001), and HCO3, BEe and K were observed between the two groups (p < 0.01). No statistically significant difference between the values of PaCO2, PH and PaO2 in the two groups were reported (p > 0.05). The results of this study confirmed that heparin 1000 and heparin 5000 units had no effects on respiratory parameters in analyzing arterial blood gases. However, the concentration of heparin had a significant effect on metabolic parameters for the analysis of arterial blood gases and electrolytes.