Transposable elements (TEs) have driven the evolution of complex traits in eukaryotes via a range of different mechanisms. Ciliated protozoa (ciliates) are a valuable model eukaryote in which several groundbreaking discoveries have been made over the years. Their unusual life cycle and genome organisation have led to a unique co-evolution with transposable elements (TEs), making them a fascinating system in which to study TE insertion, silencing and domestication. In this chapter, we discuss non-Mendelian inheritance and evolution in ciliates, with a focus on TEs.