Recent advances in DNA microarray technology have enabled eukaryotic replication to be studied at whole-chromosome and genome-wide levels. These studies have provided new insights into the mechanisms that influence origin selection and the temporally co-ordinated activation of replication initiation from these sites. Here we describe multiple microarray-based approaches that have been used to study DNA replication in both S. cerevisiae and higher eukaryotes. We have also compiled the data from the yeast microarray-based replication studies to generate a comprehensive list of origins that has been verified in three independent studies. The comprehensive nature of the microarray-based studies has revealed clear connections between chromosome organization and the pattern of replication. For example, in yeast, the centromeric proximal sequences are consistently early replicating and telomeric regions are consistently late replicating. The metazoan studies reveal a recurring theme of gene-dense transcriptionally active regions of the genome replicating before gene-sparse regions. In addition to the insights they have provided already, microarray-based replication assays combined with genetic analysis will provide a powerful new approach to define the mechanisms that regulate replication origin function.