The extracellular matrix (ECM) is proposed to play critical roles in organ morphogenesis through the stabilization and/or sequestration of signaling factors and adhesion molecules, and by maintaining organ integrity. As a first step toward understanding molecules involved in ECM modification and maturation, we have examined the embryonic expression profiles of ten prolyl 4-hydroxylase alpha subunit (PH4alpha)-related genes. Prolyl 4-hydroxylases (PH4) catalyze the formation of 4-hydroxyproline in collagens, the major components of the ECM, and are implicated in the hydroxylation of proline in several other secreted proteins. To date, two alpha subunit proteins have been described in both humans (PHalphaI and PHalphaII) and worms (PHY-1/DPY-18 and PHY-2), whereas only a single Drosophila alpha subunit has been identified. The ten PH4alpha-related genes described in this study are clustered in a 183-kb region near the tip of chromosome arm 3R and include the previously described Drosophila alpha subunit gene. Six of the ten PH4alpha genes in the cluster have tissue-specific embryonic expression. PH4alphaSG1 and PH4alphaSG2 are expressed in the salivary gland, PH4alphaMP is expressed in mouth-part precursors, PH4alphaPV is expressed in the proventriculus, and CG9698-E is expressed in the epidermis. PH4alphaEFB is expressed more broadly, with expression in the anterior and posterior midgut primordia, the fat body, the hemocytes and the epidermis. The expression profiles of these PH4alpha-related genes suggest that tissue-specific ECM modifications may be critical to organ formation and/or function.