We have studied some characteristics of clear air echoes in the lower stratosphere and troposphere from simultaneous observations of vertical echo power and temperature profiles. The vertical echo power has been oversampled every 75 m with a height resolution of 150 m by the middle and upper atmosphere (MU) radar (35°N, 136°E). During the radar observations a radiosonde was launched at the MU radar site in order to measure temperature, humidity, and pressure with a height resolution of a few tens of meters, from which the mean gradient of generalized potential refractive index, M, was determined. In the lower troposphere (below 10 km altitude), M is enhanced owing to humidity by about 10–20 dB, and its fine structure is mainly determined by the vertical gradient of humidity. The relatively large time-height variation of tropospheric echo power seems to be attributed to rapid changes in the humidity profile. On the other hand, in the upper troposphere (above 10 km altitude) and stratosphere the vertical structure of M is mainly determined by the Brunt-Väisälä frequency and air density, where the former determines fine vertical structure of M and the latter the gradual decrease in M with a scale height of about 7 km. The measured M2 profile agrees well with the vertical echo power profile down to the radar height resolution of 150 m. That is, the vertical structure of the reflection coefficient is mainly determined by M2, and therefore the energy density of 3-m scale fluctuations E(2k) seems to be distributed uniformly with height. The vertical spacing of intense reflection layers usually ranges from 500 m to a few kilometers, which corresponds to the dominant vertical scale of fluctuations in the Brunt-Väisälä frequency profile. The vertical distribution of intense reflection layers seems to be explained by a predominance of a saturated vertical wave number spectrum of gravity waves with a slope of −3 and a dominant vertical scale of a few kilometers.