Studies have shown a link between living on a farm, exposure to microbial components (e.g., endotoxins or beta-d-glucans), and a lower risk for allergic diseases and asthma. Due to the lack of validated sampling methods, studies of asthma and atopy have not relied on exposure assessment based on culture techniques. Our objective was therefore to compare several dust sampling methods for the detection of cultivable-microorganism exposure in stables. Sixteen French farms were sampled using four different methods: (i) active air sampling using a pump, (ii) passive dust sampling with a plastic box, (iii) dust sampling with an electrostatic dust fall collector (wipe), and (iv) dust sampling using a spatula to collect dust already settled on a windowsill. The results showed that collection of settled dust samples with either plastic boxes or wipes was reproducible (pairwise correlations, 0.72 and 0.73, respectively) and resulted in highly correlated results (pairwise correlation between the two methods, 0.82). We also found that settled dust samples collected with a plastic box correctly reflected the composition of the samples collected in the air of the stable when there was no farmer activity. A loss of microbial diversity was observed when dust was kept for 3 months at room temperature. We therefore conclude that measurement of viable microorganisms within a reasonable time frame gives an accurate representation of the microbial composition of stable air.