Developmental programs are tightly regulated networks of molecular and cellular signaling pathways that orchestrate the formation and organization of tissues and organs during organismal development. However, these programs can be disrupted or activated in an untimely manner, or in the wrong tissues, and this can lead to a host of diseases. This aberrant reactivation can occur due to a multitude of factors, including genetic mutations, environmental influences, or epigenetic modifications. Consequently, cells may undergo abnormal growth, differentiation, or migration, leading to structural abnormalities or functional impairments at the tissue or organismal level. This Subject Collection of The FEBS Journal on Developmental Pathways in Disease highlights 11 reviews and three research articles that cover a broad array of topics focused on the role of signaling pathways critical for normal development that are deregulated in human disease.