The first observations of the recently completed Wisconsin H alpha Mapper (WHAM) facility include a study of emission lines from high-velocity clouds in the M, A, and C complexes, with most of the observations on the M I cloud. We present results including clear detections of H alpha emission from all three complexes with intensities ranging from 0.06 to 0.20 R. In every observed direction where there is significant high-velocity H I gas seen in 21 cm emission, we have found associated ionized hydrogen emitting the H alpha line. The velocities of the H alpha and the 21 cm emissions are well correlated in every case except one, but the intensities are not correlated. There is some evidence that the ionized gas producing the H alpha emission envelopes the 21 cm-emitting neutral gas, but the H alpha "halo," if present, is not large. If the H alpha emission arises from the photoionization of the H I clouds, then the implied incident Lyman continuum flux F-LC at the location of the clouds ranges from 1.3 to 4.2 x 10(5) photons cm(-2) s(-1). If, on the other hand, the ionization is due to a shock arising from the collision of the high-velocity gas with an ambient medium in the halo, then the density of the preshocked gas can be constrained. We have also detected the [S II] lambda 6716 line from the M I cloud and have evidence that the [S II] lambda 6716 to H alpha ratio varies with location on the cloud.