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Abstract The behaviour of the Balmer lines in the spectra of 13 Apstars has been investigated. It was found that all the investigated stars show the variation in the hydrogen line contours, equivalent widths and the variation of lg ne and lg (N02H) as well. The curves of the equivalent width variations during the period have several maxima and minima whereas the light curves have no more than two maxima and minima. While transiting from one line to another the position of the extremum coincides very seldom. The electron concentration determined for all stars by the Balmer line profiles has the minimum in those places where the spots with the higher concentration of one or another element are situated. It is possible that the most intensive spot of the definite chemical element is responsible for the minimum of lg ne. The hydrogen line profiles show that the lines are always wider and deeper at the moment of minimum light than at the moment of its maximum. In some cases the hydrogen line center has a complex profile. The measurements of the radial velocity of the absorptional peak in the center of the hydrogen lines of Hγ, Hδ, H show the existence of rapid changes in 17 Com A and HD 224 801 with a characteristic time scale equal to 71 minutes and 6 hours, respectively.