Aquaporins are membrane proteins that facilitate water transport across the membranes in various microorganisms, plants and animals. Plant aquaporins are divided into four groups based on the amino acid sequence similarities and intracellular localization: plasma membrane intrinsic proteins (PIPs), tonoplast intrinsic proteins (TIPs), nodulin-like intrinsic proteins (NIPs) and small basic intrinsic proteins (SIPs). We found 35 EST sequences homologous to 3' and 5' termini of the partial cDNA of P. nil in the GenBank NCBI database. cDNA encoding full length aquaporin of P. nil was cloned with the use of the reverse transcription-polymerase chain reaction (RT-PCR). The 1189 bp full length cDNA sequence of aquaporin P. nil (PnPIP1) was obtained. Analysis of protein hydropathy indicated that cloned part of PnPIP1 contained the NPA motif (Asn-Pro-Ala) that is present in all known aquaporins. The amino acid sequence of the PnPIP1 protein exhibits 90, 89 and 88% sequence similarity to Petunia x hybrida, Nicotiana excelior and Fraxinus excelsior aquaporins respectively. We showed that the EST database is a useful tool for identification of the complete cDNA of known genes.