Aquaporins facilitate water transport over cellular membranes, and are therefore believed to play an important role in water homeostasis. In higher plants aquaporin-like proteins, also called major intrinsic proteins (MIPs), are divided into five subfamilies. We have previously shown that MIP transcription in Arabidopsis thaliana is generally downregulated in leaves upon drought stress, apart from two members of the plasma membrane intrinsic protein (PIP) subfamily, AtPIP1;4 and AtPIP2;5, which are upregulated. In order to assess whether this regulation is general or accession-specific we monitored the gene expression of all PIPs in five Arabidopsis accessions. The overall drought regulation of PIPs was well conserved for all five accessions tested, suggesting a general and fundamental physiological role of this drought response. In addition, significant differences among accessions were identified for transcripts of three PIP genes. Principal component analysis showed that most of the PIP transcriptional variation during drought stress could be explained by one variable linked to leaf water content. Promoter-GUS constructs of AtPIP1;4, AtPIP2;5 and also AtPIP2;6, which is unresponsive to drought stress, had distinct expression patterns concentrated in the base of the leaf petioles and parts of the flowers. The presence of drought stress response elements within the 1.6-kb promoter regions of AtPIP1;4 and AtPIP2;5 was demonstrated by comparing transcription of the promoter reporter construct and the endogenous gene upon drought stress. Analysis by ATTED-II and other web-based bioinformatical tools showed that several of the MIPs downregulated upon drought are strongly co-expressed, whereas AtPIP1;4, AtPIP2;5 and AtPIP2;6 are not co-expressed.