Ciliated protozoa have two functionally and structurally distinct nuclei, a somatic macronucleus (MAC) and a germline micronucleus (MIC), in the same cytoplasm. Nuclear dimorphism is one of the most mysterious puzzles in Ciliate Biology: how these two distinct nuclei are formed in a single cell remains to be solved. Toward this end, we have studied structural differences between the MAC and MIC in Tetrahymena thermophila and have found that the two nuclei have distinctive nuclear pore complexes. Importantly, this difference affects the nuclear entry of nucleus-specific nuclear proteins. This finding suggests that the nuclear pore complex together with the nuclear transport system may be one of the key factors that generate the nuclear dimorphism in T. thermophila. In this review, I will focus on the differences between the MAC and MIC nuclear pore complexes and discuss how these difference can cause nucleus-specific nuclear transport leading to nuclear dimorphism in ciliates.