In order to account for the experimental observation that some amines form clathrate hydrates but that alcohols inhibit hydrate formation, we investigate the stability of clathrate hydrates which encage highly polar guest molecules by examining potential energy local minimum structures and also thermally excited structures. First, we examine the local minimum structure at which the total potential energy has a minimum value for amine and alcohol hydrates and inquire whether, in the absence of thermal fluctuations, the conditions for true-clathrate hydrates are satisfied. The local minimum structures of alcohol hydrates are distinguished from those of stable clathrate hydrates of structures I and II, while amine hydrates hold the host lattice of clathrate hydrates. We argue that the difference between the magnitude of the partial charge on the hydrogen atom of the hydroxyl and amino groups plays a much more significant role in the stability of both kinds of clathrate hydrates than the difference in molecular geometry does. Second, we examine kinetic stability by molecular dynamics simulation. Near room temperature the host lattice structure encaging amine remains intact. This is in contrast to the alcohol hydrate, which begins to melt easily with thermal excitation. Interesting is the finding that very long-time-scale (similar to 100 ps) fluctuations of the host potential energy is observed, as well as fast oscillations caused by temporary partial defects in the host network. Clathrate hydrates of polar guest molecules may experience an unstable state in which the host hydrogen-bonded network is partially broken and guest-host hydrogen-bond generation occurs but the stable state of their host lattices is again restored.