Hypoxanthine-guanine phosphoribosyltransferase (HGPRT) deficiency is transmitted as an X-linked recessive trait. Female carriers are asymptomatic and the carrier diagnosis is usually performed by determining HGPRT activity in hair roots. This technique does not allow a non-carrier state diagnosis with absolute certainty and has other limitations such as obtaining non-viable hair roots. The knowledge of the genetic mutation in three Spanish families with HGPRT deficiency, enabled us to perform the genetic diagnosis of the carrier state in 10 female subjects at risk and one female fetus. The genetic diagnosis has been performed by analyzing the differences between the mutant and the normal allele with respect to the restriction pattern. When the restriction pattern showed no differences, this has been created by directed mutagenesis. With this methodology we confirmed that a newborn of a known carrier female of HGPRT deficiency was healthy. In all cases the diagnosis could be established with great fiability in a mean time of 24 to 48 hours. We report the first genetic diagnosis of the carrier state for the HGPRT deficiency performed in Spain.