We investigated the family of a 3-year-old boy with manifestations of the Martin-Bell syndrome (MBS). His 17-year-old cousin had classic manifestations of MBS and was fragile X [fra(X)] positive. The 3-year-old boy was fra(X) negative. Linkage analysis with probes flanking the fra(X) region indicated that these cousins had the same X chromosome inherited from a normal grandfather. The DNA and cytogenetic analyses suggest that limitations in the ability to detect the fra(X) mutation cytogenetically may be responsible for fra(X)-negative MBS; or, alternatively, that a crossover occurred between a locus determining the MBS phenotype and one determining fra(X) expression.