<b><i>Introduction:</i></b> Spinal muscular atrophy (SMA) is a debilitating neuromuscular disorder caused by biallelic deletion of the <i>SMN1</i> gene. Nusinersen, an antisense oligonucleotide delivered intrathecally, binds to the pre-mRNA of <i>SMN1</i>’s pseudogene, <i>SMN2</i>, to prevent exon skipping and produce functional SMN protein to compensate for the deficiency caused by <i>SMN1</i> deletion. <b><i>Case Presentation:</i></b> We reviewed 15 cerebrospinal fluid (CSF) cytology specimens from 8 patients receiving nusinersen for SMA. Macrophages with peculiar inclusions (“nusinophages”) were seen in 8 specimens from 4 of the patients: 1 infant and 3 children with SMA type 1. This finding has only previously been reported in adults with SMA types 2 and 3 and in 2 infants with SMA type 1. <b><i>Discussion/Conclusion:</i></b> Specimens containing nusinophages had a significantly higher proportion of macrophages and lower proportion of lymphocytes than those in which nusinophages were not detected. The macrophage inclusions do not represent iron or microorganisms and instead are composed, at least in part, of glycosaminoglycans. Because CSF is a common specimen type, cytotechnologists and cytopathologists need to be aware of these inclusions, so they do not interpret them erroneously as evidence of infection or hemorrhage, especially in light of the fact that oligonucleotide therapy has been approved for a variety of conditions and is currently under investigation for intrathecal delivery in several other neurodegenerative disorders.