The conformational and structural properties of the inhalational anesthetic isoflurane (1-chloro-2,2,2-trifluoroethyl difluoromethyl ether) have been probed in a supersonic jet expansion using Fourier-transform microwave (FT-MW) spectroscopy. Two conformers of the isolated molecule were identified from the rotational spectrum of the parent and several (37)Cl and (13)C isotopologues detected in natural abundance. The two most stable structures of isoflurane are characterized by an anti carbon skeleton (τ(C(1)-C(2)-O-C(3)) = 137.8(11)° or 167.4(19)°), differing in the trans (AT) or gauche (AG) orientation of the difluoromethyl group. The conformational abundances in the jet were estimated from relative intensity measurements as (AT)/(AG) ≈ 3:1. The structural preferences of the molecule have been rationalized with supporting ab initio calculations and natural-bond-orbital (NBO) analysis, which suggest that the molecule is stabilized by hyperconjugative effects. The NBO analysis of donor-acceptor (LP → σ*) interactions showed that these stereoelectronic effects decrease from the AT to AG conformations, so the conformational preferences can be accounted for in terms of the generalized anomeric effect.