Objective While bacterial DNA and synthetic oligodeoxynucleotides (ODN) containing unmethylated CpG dinucleotides with specific flanking sequences (CpG motif) are well described activators of murine immune cells, CpG motifs for activating human immune cells remain unclear. This study is to delineate CpG motifs and CpG ODN for activating human immune cells. Methods A panel of CpG ODN containing two copies of CpG motifs was screened for their capacity to stimulate human B lymphocytes to secret IgM. Then CpG ODN containing human CpG motifs was designed and tested to identify the sequence of high immunostimulatory activity for human immune cells. Results The study revealed that 5′ GTCGTT 3′ and 5′ GTCGTC 3′ were two potent CpG motifs for human immune cells, and other four CpG motifs, 5′ GACGTT 3′, 5′ GACGTC 3′, 5′ GGCGTT 3′ and 5′ GGCGTC 3′, had moderate activities. The second nucleotide in optimal human CpG motifs was thymidine, while in less active human CpG motifs or optimal murine CpG motifs, it was purines. Based on this finding, many CpG ODN were designed and identified as high immunostimulatory sequences for human B lymphocytes. Conclusion Some CpG motifs and CpG ODN are potential activators of human immune cells.