Context. The variability in IRC+10216, the envelope of the asymptotic giant branch (AGB) star CW Leo, has attracted increasing attention in recent years. Studying the details of this variability in the molecular emission required a systematic observation program. Aims. We aim to reveal and characterize the periodical variability of the rotational lines from several molecules and radicals in IRC+10216, and to compare it with previously reported IR variability. Methods. We carried out systematic monitoring within the ~80–116 GHz frequency range with the IRAM 30 m telescope. Results. We report on the periodical variability in IRC+10216 of several rotational lines from the following molecules and radicals: HC₃N, HC₅N, CCH, C₄H, C₅H, and CN. The analysis of the variable molecular lines provides periods that are consistent with previously reported IR variability, and interesting phase lags are revealed that point toward radiative transfer and pumping, rather than chemical effects. Conclusions. This study indicates that observations of several lines of a given molecule have to be performed simultaneously or at least at the same phase in order to avoid erroneous interpretation of the data. In particular, merging ALMA data from different epochs may prove to be difficult, as shown by the example of the variability we studied here. Moreover, radiative transfer codes have to incorporate the effect of population variability in the rotational levels in CW Leo.