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We have recently witnessed the rapid development of various single-cell sequencing technologies. Pioneering single cell assays are now available for the profiling of genome, epigenome, and transcriptome. Single-cell sequencing technologies provide multi-dimensional information on early embryonic development in humans and in clinical contexts where specimens are scarce. Here, we review several available techniques and their applications in reproductive medicine. Continuing development of multimodal single-cell sequencing measurement techniques in combination with multi-omics assays will provide comprehensive profiles of an individual cell and lead to the targeted therapy for reproductive disorders and infertility.