Previous reports have established that the telomeric copy of the survival motor neuron (SMN^T) gene and the intact copy of the neuronal apoptosis inhibitory protein (NAIP) gene are preferentially deleted in patients with spinal muscular atrophy (SMA). Although deletions or mutations in the SMN^T gene are most highly correlated with SMA, it is not clear to what extent NAIP or other genes influence the SMA phenotype, or whether a small fraction of SMA patients actually have functional copies of both SMN^T and NAIP. To evaluate further the part of SMN^T in the development of SMA, we analyzed 280 asymptomatic SMA family members for the presence or absence of SMN^T exons 7 and 8. We report the following observations: (i) 4% of the sample harbored a polymorphic variant of SMN^T exon 7 that looks like a homozygous deletion; (ii) approximately 1% of the parents are homozygously deleted for both exons 7 and 8; (iii) one asymptomatic parent lacking both copies of SMN^T exons 7 and 8 displays a ‘subclinical phenotype’ characterized by mild neurogenic pathology; (iv) another asymptomatic parent lacking both SMN^T exons showed no signs of motor neuron disorder by clinical and neurodiagnostic analyses. The demonstration of polymorphic variants of exon 7 that masquerade as homozygous nulls, and the identification of SMA parents who harbor two disease alleles, serve as a caution to those conducting prenatal tests with these markers.