A better understanding of physician practices in requesting stool samples for patients with acute gastroenteritis (AG) is needed to more accurately interpret laboratory-based surveillance data. A survey was conducted in General Practitioners (GPs) between August 2013 and July 2014 to estimate the proportion of stool samples requested for patients with AG and to identify factors associated with GP requests for a stool sample. National health insurance (NHI) data together with surveillance data from a French Sentinel GP network were also used to estimate the proportion of stool samples requested. This proportion was estimated at 4·3% in the GP survey and 9·1% (95% confidence interval 8·7-9·6) using NHI data. Multivariate analysis indicated that the ratio of stool samples requested was almost five times higher in patients with bloody diarrhoea and 10-20 times higher in patients with a long duration of illness before consultation. Laboratory-based surveillance data underestimates the actual burden of disease as fewer than one in 10 AG cases consulting their GP will be requested to submit a stool sample for laboratory testing. This underestimation varies by pathogen as stool samples are more frequently requested for severe illness.