Homologous recombination (HR) is essential for cellular survival in mammals. In this review, the substrates for HR, the pathways of repair, and their end products (i.e. sister chromatid exchange (SCE), gene conversion, deletions or tandem duplications) are discussed. HR is involved in the repair of DNA double-strand breaks (DSBs) and DNA lesions that occur at replication forks. A classical DSB may result in deletions, tandem duplications or gene conversion following two-end recombination repair. In contrast, a SCE may be the result of one-end recombination repair at a collapsed replication fork, i.e. a single-strand break converted into a DSB at a replication fork. Recombination repair at a stalled replication fork may occur in the absence of a DSB intermediate and may result in either SCE or gene conversion. Finally, substrates and pathways involved in spontaneous HR are discussed.