A rat farnesyl pyrophosphate (FPP) synthetase cDNA was used to study the expression of FPP synthetase mRNA levels during spermatogenesis in the rat. RNA blot analysis showed an increase in the level of FPP synthetase transcripts during postnatal development of rat testes. The increase is due to the appearance of longer testis-specific FPP synthetase transcripts as assayed by primer extension mapping. In situ hybridization analysis of adult rat testis sections with an FPP synthetase antisense probe showed that FPP synthetase mRNA levels are greatly enriched in the haploid round spermatidis at stages 7 to 8 of the seminiferous epithelium. These results show that FPP synthetase transcripts in testis are expressed at high levels in haploid male germ cells in a stage-specific manner.