The article provides an in-depth review of the molecular and structural aspects of cilia, particularly focusing on the ciliopathies—diseases caused by defects in cilia or their associated proteins. Cilia are essential cellular organelles that can be motile or non-motile, and their dysfunction leads to a wide range of human diseases. The review highlights the importance of understanding the basal body, axoneme, and transition zone in ciliogenesis and ciliary function. It discusses the roles of key proteins and complexes, such as the IFT machinery, transition zone proteins, and BBSome, in ciliary assembly and signaling. The article also explores the genetic heterogeneity of ciliopathies, distinguishing between first-order (directly involved in ciliary structure or function) and second-order (involved in non-ciliary processes affecting ciliary function) ciliopathies. Additionally, it examines the impact of ciliary defects on sensory functions, development, and physiological processes, and outlines strategies for identifying new ciliopathy-associated proteins and genes. The authors emphasize the importance of model organisms and interdisciplinary approaches in advancing the understanding of ciliopathies and their underlying mechanisms.The article provides an in-depth review of the molecular and structural aspects of cilia, particularly focusing on the ciliopathies—diseases caused by defects in cilia or their associated proteins. Cilia are essential cellular organelles that can be motile or non-motile, and their dysfunction leads to a wide range of human diseases. The review highlights the importance of understanding the basal body, axoneme, and transition zone in ciliogenesis and ciliary function. It discusses the roles of key proteins and complexes, such as the IFT machinery, transition zone proteins, and BBSome, in ciliary assembly and signaling. The article also explores the genetic heterogeneity of ciliopathies, distinguishing between first-order (directly involved in ciliary structure or function) and second-order (involved in non-ciliary processes affecting ciliary function) ciliopathies. Additionally, it examines the impact of ciliary defects on sensory functions, development, and physiological processes, and outlines strategies for identifying new ciliopathy-associated proteins and genes. The authors emphasize the importance of model organisms and interdisciplinary approaches in advancing the understanding of ciliopathies and their underlying mechanisms.