A preterm neonate at 29-week gestational age was born with intrauterine growth restriction, severe pancytopaenia and gross skeletal dysplasia. Antenatal screening bloods, TORCH/parvovirus tests and karyotype were unremarkable. Postnatally, he had normal microarray comparative genomic hybridization and serum B12/folate levels, and human immunodeficiency virus and cytomegalovirus polymerase chain reaction and antoimmune screening were negative. Targeted gene testing for Shwachman–Diamond syndrome (SDS) revealed the pathognomic mutation (c.183_184delTAinsCT). His postnatal clinical course was complicated by: (i) Ventilator dependency because of a combination of a pathologically compliant chest wall and preterm-associated chronic lung disease. (ii) Progressive bone marrow failure, resulting in transfusion dependence and profound neutropenia associated with recurrent sepsis. (iii) Gastrointestinal failure and TPN dependency. (iv) Poor postnatal growth with weight/length/head circumference all <3rd centile. (v) Prognostication was complicated by the lack of published literature on the presentation of SDS in a preterm infant. However, because of inexorable progression of multiorgan failure, intensive care was withdrawn on day 54 of life. SDS is a rare autosomal recessive disorder characterised by haematological abnormalities, skeletal dysplasia and exocrine pancreatic dysfunction. Neonatal presentation is thought to be extremely rare. However, with the availability of genetic testing, it has now become clear that because of overlap in clinical presentation, term-born infants with skeletal dysplasia and severe respiratory distress may initially be misdiagnosed as asphyxiating thoracic dystrophy. This case report highlights the complexities of preterm birth complicating clinical manifestations of SDS.