Proline-rich cell wall proteins are widely spread in plants and are believed to function by modeling the architecture of the cell wall surrounding specific cell types. Five genes encoding proline-rich proteins were isolated from cotton cDNA libraries. The most common characteristic of these proteins is the abundant proline residues that occur in repeating motifs of at least two consecutive Pros. Based on amino acid composition, repetitive motifs and domain organization, the five members can be divided into two subgroups: one group similar to common PRPs including GhPRP3, GhPRP6, GhPRP5 and GhPRP4 was composed of two domains, an N-terminal hydrophobic domain (or signal peptide) followed by a proline-rich domain containing different proline-rich repetitive motifs; the other group different from common PRPs including GhPRPL lies in it contains an N-terminal hydrophilic domain, eight repetitive copies of pentapeptide (similar to PPKKE) lies in the C-terminal domain. Expression studies of the six GhPRPs have been carried out by quantitative realtime RT-PCR. The results showed that GhPRP3 and GhPRP5 were preferentially expressed in 10 dpa fiber, little transcripts was detected in other tissues examined. GhPRPL highly expressed in cotyledons, whereas smaller or negligible amounts of its transcripts were detected in other tissues. The remaining two genes, GhPRP4 and GhPRP6, were expressed in all the tissues analysed, but their transcript level is different. GhPRP4 mRNA is most abundant in hypocotyls, and then in anther, while GhPRP6 expressed highly in fiber, and then in 10 dpa ovule. Furthermore, the results showed that the fiber-specific GhPRP3 and GhPRP5 were also developmentally regulated, suggesting that the genes may play important roles during cotton fiber development.