Abstract We karyometrically investigated the nucleus suprachiasmaticus (SCN) which had been manipulated in several ways in order to analyze the functional importance of the pineal gland on the primary pacemaker of mammals in the course of the year. The manipulation modes were (i) pinealectomy (PX), and (ii) sympathetic denervation of the pineal by bilateral extirpation of the upper cervical ganglia (ganglion ectomy, GX). Additionally, the influence of the inactivated pineal, obtained through hypothyroidism which was realized by (iii) subtotal thyroidectomy (TX), was also investigated. With respect to annual oscillations the results of our investigations were able to illustrate the following. (1) The SCN consists of at least two parts (ventrolateral and dorsomedial) each with different functions and relationships. The nuclei of the ventrolateral cells are bigger and there are many indications both in our own research and from literature that the neurons of this part are involved in the generation of rhythms. (2) The size of the cell nuclei of the ventrolateral part shows annual patterns. In the course of the year the maxima of the nuclear volume were registered in March and September (bimodal pattern, equinox, L:D = 12:12). PX, GX or TX only negligibly changed the bimodal annual pattern. However, in comparison the smallest cell nuclei were registered in the winter (short day). The much smaller cell nuclei of the dorsomedial part likewise show bimodal patterns but only in the experimental groups. The control group of this part shows an unimodal annual curve with a minimum at long-day conditions (June. L:D = 16:8). (3) All manipulations which inactivated the pineal or reduced the content of melatonin (PX, GX, and TX) were followed by an increase (activation) of cell nuclei of the SCN. In contrast to these effects, an increase of thyroxine (by exposure to cold), has an opposite effect (not documented here). In conclusion these results indicate, without a doubt, that a negative correlation exists, functionally, between the SCN and the pineal (in the same annual experiment the nuclear size of the pinealocytes was increased, under short-day conditions in December, and decreased under long-day circumstances in June). Additionally, it could be shown that the degree of negative correlation between the pineal and the SCN was seasonally dependent. The lowest effects of PX, GX and TX were registered at short-day conditions (December, L:D = 8:16).