[Abridged] We present the first comprehensive study of short-timescale chromospheric H-alpha variability in M dwarfs using the individual 15 min spectroscopic exposures for 52,392 objects from the Sloan Digital Sky Survey. Our sample contains about 10^3-10^4 objects per spectral type bin in the range M0-M9, with a total of about 206,000 spectra and a typical number of 3 exposures per object (ranging up to a maximum of 30 exposures). Using this extensive data set we find that about 16% of the sources exhibit H-alpha emission in at least one exposure, and of those about 45% exhibit H-alpha emission in all of the available exposures. Within the sample of objects with H-alpha emission, only 26% are consistent with non-variable emission, independent of spectral type. The H-alpha variability, quantified in terms of the ratio of maximum to minimum H-alpha equivalent width (R_EW), and the ratio of the standard deviation to the mean (sigma_EW/<EW>), exhibits a rapid rise from M0 to M5, followed by a plateau and a possible decline in M9 objects. In particular, R_EW increases from a median value of about 1.8 for M0-M3 to about 2.5 for M7-M9, and variability with R_EW>10 is only observed in objects later than M5. For the combined sample we find that the R_EW values follow an exponential distribution with N(R_EW) exp[-(R_EW-1)/2]; for M5-M9 objects the characteristic scale is R_EW-1approx 2.7, indicative of stronger variability. In addition, we find that objects with persistent H-alpha emission exhibit smaller values of R_EW than those with intermittent H-alpha emission. Based on these results we conclude that H-alpha variability in M dwarfs on timescales of 15 min to 1 hr increases with later spectral type, and that the variability is larger for intermittent sources.
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