Protons have long been recognized as low LET radiation in radiotherapy. However, a detailed account of LET (linear energy transfer) and RBE (relative biological effectiveness) changes with incident beam energy and depth in tissue is still unresolved. This issue is particularly important for treatment planning, where the physical dose prescription is calculated from a RBE using cobalt as the reference radiation. Any significant RBE changes with energy or depth will be important to incorporate in treatment planning. In this paper we present microdosimetry spectra for the proton beam at various energies and depths and compare the results to cell survival studies performed at Loma Linda. An empirically determined biological weighting function that depends on lineal energy is used to correlate the microdosimetry spectra with cell survival data. We conclude that the variations in measured RBE with beam energy and depth are small until the distal edge of the beam is reached. On the distal edge, protons achieve stopping powers as high as 100 keV/micron, which is reflected in the lineal energy spectra taken there. Lineal energy spectra 5 cm beyond the distal edge of the Bragg peak also show a high LET component but at a dose rate 600 times smaller than observed inside the proton field.