Ciliogenesis is divided into four stages: (1) generation of centrioles, (2) migration of duplicated centrioles, (3) formation of the basal body-associated structures, and (4) elongation of cilia. The ultrastructural profile of ciliogenesis is fundamentally the same among various kinds of animal species. In acentriolar centriologenesis, centrioles are generated around deuterosomes by the use of fibrous granules. Components of the centriolar precursor structures, and genes that regulate the differentiation of ciliated cells, have been revealed. Ciliary abnormalities are classified into two categories: specific congenital defects of ciliary structure and acquired nonspecific anomalies of the ciliary apparatus. When ciliogenesis is disturbed, various nonspecific ciliary abnormalities develop in the cell. Inhibition of centriole migration results in the development of intracytoplasmic axonemes, cilia within periciliary sheaths, and intracellular ciliated vacuoles. Swollen cilia and the bulging type of compound cilia are formed during ciliary budding and elongation. Primary cilia can also develop from one of a pair of centrioles. They lack dynein arms and are immobile, but work as a mechanosensor and play a role during morphogenesis of the kidney. Abnormal function or structure of primary cilia results in the development of polycystic kidney disease. The axonemes of primary cilia or monocilia in the embryonic node cells are associated with dynein arms and move vortically. They have a role in determining the left-right (L-R) asymmetry of the fetus. This review also discusses the ciliogenesis of a primary cilium in the cell.