Kidney development is a multi-step process where undifferentiated mesenchyme is converted into a highly complex organ through several inductive events. The general principles regulating these events have been under intense investigation and despite extensive progress, many open questions remain. While the metanephric kidneys of mouse and rat have served as the primary model, other organisms also significantly contribute to the field. In particular, the more primitive pronephric kidney has emerged as an alternative model due to its simplicity and experimental accessibility. Many aspects of nephron development such as the patterning along its proximo-distal axis are evolutionarily conserved and are therefore directly applicable to higher vertebrates. This review will focus on the current understanding of pronephros development in Xenopus. It summarizes how signaling, transcriptional regulation, as well as post-transcriptional mechanisms contribute to the differentiation of renal epithelial cells. The data show that even in the simple pronephros the mechanisms regulating kidney organogenesis are highly complex. It also illustrates that a multifaceted analysis embracing modern genome-wide approaches combined with single gene analysis will be required to fully understand all the intricacies.