The present study describes transcription of mRNA from genes encoding metabolic or structural proteins during excystation of Cryptosporidium parvum oocysts. RNA was harvested from C. parvum oocysts before excystation, and at 5, 10, and 15 min during excystation. Subtractive cDNA libraries were prepared by using mRNA from non-excysted C. parvum oocysts to "subtract out" mRNA from excysting oocysts. The "subtracted" cDNA was used to prepare libraries enriched for transcripts possibly involved in excystation. From these libraries, over 1,000 expressed sequence tags (ESTs) were analyzed by DNA sequencing followed by BLAST-N and BLAST-X analysis. While several gene products involved in cell metabolism and cell signaling were consistently recovered, transcription levels, as reflected by the relative number of cDNA sequences (19.2% total), were highly up-regulated in genes coding for structural proteins such as Cp2, CpTSP, CpHC10, and CpSAg. Moreover, of the greater than 1,000 clones analyzed, a high percentage (12.3%) of ESTs detected in excysting oocysts were for hypothetical C. parvum proteins (CpHyP), whose functions are presently unknown.