Comet C/1999 S4 (LINEAR) was exceptional in many respects. Its nucleus underwent multiple fragmentations culminating in the complete disruption around July 20, 2000. We present circular polarization measurements along the cuts through the coma and nucleus of the comet during three separate observing runs, in June 28-July 2, July 8-9, and July 21-22, 2000. The circular polarization was detected at a rather high level, up to 0.8%. The left-handed as well as right-handed polarization was observed over the coma with the left circularly polarized light systematically observed in the sunward part of the coma. During our observations the phase angle of the comet varied from 61 up to 122°, which allowed us to reveal variations of circular polarization with the phase angle. Correlation between the degree of circular polarization, visual magnitude, water production rate, and linear polarization of comet C/1999 S4 (LINEAR) during its final fragmentation in July 2000 was found.The mechanisms that may produce circular polarization in comets and specifically in comet C/1999 S4 (LINEAR) are discussed and some tentative interpretation is presented.