Greenhouse gases (GHG) emissions from two naturally-ventilated free-stall dairy barns were measured continuously during a three-month study period (May, July and September, 2009). Barn 1 (B1) housed 400 fresh cows, while Barn 2 (B2) housed 850 lactating cows. Air samples of inlet and outlet of the barns for measurement of GHG (carbon dioxide, nitrous oxide and methane) concentrations were delivered to a photoacoustic gas analyzer (INNOVA model 1412) using a custom-made gas sampling system. Ventilation rates in the barns were determined using three dimensional ultrasonic anemometers mounted on air inlets and outlets. Emissions of carbon dioxide averaged 23.14 in B1 and 18.53kg-CO 2/cow/d in B2, respectively. Methane emissions averaged 326.5 in B1 and 374.5 g-CH4/cow/d in B2. The respective emissions of nitrous oxide in B1 and B2 were 16.00 and 7.86 g-N2O/cow/d, respectively. Emissions of carbon dioxide and methane in both barns were indicated the similar levels. On the other hand, the significant difference in nitrous oxide emissions observed in the two barns was explained by management differences. The half of Barn 1 also did not have stalls and animals on this pen thus rested on dirt. Cows' urine deposited on this dirt was thus rarely removed and explained the significantly higher emissions of N2O from this barn (B1). The correlation between carbon dioxide and nitrous oxide was considerably higher than that with methane emissions, R2 ranged from 0.82 to 0.98.