Ciliated protozoa have two distinct nuclei, germinal micronuclei and somatic macronuclei. Macronuclei are transcriptionally active, but micronuclei are almost inert. To know whether micronuclei have any function in conjugation of Paramecium caudatum, expression of the conjugation-specific nuclear antigen, CSN-1, in amicronucleate cells during conjugation was examined. Micro- (mic) and amicronucleate (amic) cells were conjugated in three combinations (mic-mic, mic-amic and amic-amic). In conjugation of two amicronucleate cells, the cells were negative against the CSN-1 antibody by indirect immunofluorescence staining and underwent abnormal macronuclear fragmentation. These were not observed in conjugation of micronucleate cells. In conjugation between micro- and amicronucleate cells, the amicronucleate mates were negative against the antibody in the beginning, but after receiving a pronucleus from the micronucleate mates, they became positive. This indicates that the CSN-1 antigen or factors involved in the expression of the antigen can hardly pass across the fused cell membrane between conjugating cells before pronuclear exchange. The present results suggest that micronuclei have some function in expression of the CSN-1 antigen and the macronuclear fragmentation, both of which are specific events in conjugation.