Random amplified polymorphic DNA (RAPD) markers have been used in genetic studies of several plant and animal species. However, concerns exist about the reproducibility of RAPD-PCR reactions. Therefore, the use of specific 24mer primer pairs in standard PCR reactions has been suggested for reliable amplification of characterized polymorphic RAPD sequences. The purpose of this article is describe the application of the RAPD-PCR assay to genetic studies of dogs and to investigate the amplification of RAPD sequences with specific primer pairs. Of 240 decanucleotide primers tested by PCR, 34.6% resulted in amplification of at least one polymorphic fragment with samples of a Labrador retriever pedigree. We cloned and sequenced five of these RAPD fragments and synthesized specific 24mer primer pairs for each. Two primer pairs amplified a sequence exclusively from samples that were positive for the RAPD fragment, while three others amplified the respective sequence from all DNA samples. A new polymorphism was observed in the restriction digest products with Msel of one of the amplification products. None of the cloned sequences contains an open reading frame longer than 213 bases. Two sequences hybridized only to specific fragments of genomic DNA from samples that amplified the RAPD, the remaining three sequences hybridized to multiple sequences in all canine samples tested by Southern analysis. None of the five fragments hybridized to human or murine genomic DNA. Data suggested that RAPD sequences can be used as molecular markers in genetic studies of diseases in dogs. However, the use of specific primer pairs leads to loss of the RAPD polymorphism in three of five sequences tested.