Glycine amidinotransferase (AGAT or GATM), guanidinoacetate methyltransferase (GAMT) and creatine transporter (CT1) are three proteins involved in the synthesis and uptake of creatine. The expression patterns of these three genes were examined in zebrafish embryos by whole mount in situ hybridization followed by histological sectioning. Expression of agat first appeared in the yolk syncytial layer (YSL) at the gastrula stage and was progressively up regulated during gastrulation. As development proceeds, agat was expressed in the mature somites during the segmentation stage and in the liver at 48 hpf. gamt showed a similar expression pattern to that of agat during embryogenesis. It was first detected in the center of the yolk from the cleavage to the gastrula stage. At the bud stage, its expression shifted to the YSL. gamt was also transiently expressed in the mature somites from 16 hpf to 24 hpf and became strongly expressed in the liver and in epithelial cells of the gut at 48 hpf. ct1 was initially uniformly expressed from the cleavage to the early segmentation stage; it was then strongly expressed in all the somites till 30 hpf and in the gut of 48 hpf embryos. However, ct1 transcripts also appeared in the central nervous system during the segmentation stage, but not in the YSL, the yolk or the liver. Our data reveal for the first time distinct and unique patterns of expression of the creatine metabolism genes agat, gamt and ct1 during zebrafish embryogenesis.