Little is known of the early stages of human follicular development and the complex processes that regulate follicular growth. To identify genes of potential importance, we analysed follicle-related transcripts in five populations of isolated size-matched human preantral follicles by microarray analysis. Oocyte-specific genes were found to be the most abundant and differentially expressed transcripts and included germ cell transcription factors LHX8 and SOHLH2 which were significantly down-regulated during preantral follicle development. Differentially expressed genes also included transcription factors of NOTCH signalling, IGF2, orphan nuclear receptor LRH-1, and homeobox gene HOXA7, indicating potentially important regulatory roles for these genes during early human folliculogenesis. We also found that FSHR mRNA and protein were present in the earliest stages of preantral follicles, whereas LHR was absent. In conclusion, our data identify specific oocyte and somatic genes in small human follicles that impact early follicle growth, and provide foundation for further analysis of the signalling pathways involved in early human folliculogenesis.