The apical portion of the Arabidopsis globular stage embryo gives rise to the cotyledons and the shoot apical meristem (SAM). The SHOOT MERISTEMLESS (STM) gene is required for SAM formation during embryogenesis and for SAM function throughout the lifetime of the plant. To more precisely define the development of molecular pattern in the apical portion of the embryo, and the role of the STM gene in the development of this pattern, we have examined AINTEGUMENTA (ANT), UNUSUAL FLORAL ORGANS (UFO) and CLAVATA1 (CLV1) expression in wild-type and stm mutant embryos. The transcripts of these genes mark subdomains within the apical portion of the embryo. Our results indicate that: (1) the molecular organization characteristic of the vegetative SAM is not present in the globular embryo but instead develops gradually during embryogenesis; (2) radial pattern exists in the apical portion of the embryo prior to and independent of STM with STM expression itself responding to radial information; (3) the embryonic SAM consists of central and peripheral subdomains that express different combinations of molecular markers and differ in their ultimate fates; and (4) STM activity is required for UFO expression, STM is required for maintenance but not onset of CLV1 expression and the pattern of ANT expression is independent of STM.