Exhaled breath can be used for early detection and diagnosis of diseases, monitoring metabolic activity, and precision medicine. In this work, we design and simulate a microwave sensor in which thin graphene aerogels are integrated into rectangular microwave waveguides. Graphene aerogels are ideal sensing platforms for gases and volatile compounds as they combine extremely high surface-to-volume ratio and good electrical conductivity at RF and microwave frequencies. The latter is modified by exposure to different gases, and -when integrated into a waveguide-these changes result in significant shifts in transmission and reflection scattering parameters. We model the aerogel as a graphene grid with hexagonal openings of size 22.86x10.16x0.1 mm 3 , characterized by an air volume equal to about 90% of its entire volume. This grid is used as a building block for modeling thicker samples (up to 9 mm). To simulate the variation in the dynamic conductivity of the graphene sheets as a consequence of the absorption of gaseous molecules, a sweep of the chemical potential from 0.0 eV to 0.5 eV with steps of 0.1 eV was used. The results show a significant variation of the waveguide transmission scattering parameters resulting from the gas-induced modification of the graphene conductivity, and hence the potential of the proposed sensor design for breath analysis.