We report the expression analysis of bone marrow (BM) cells of patients with Shwachman-Diamond syndrome (SDS), in relation to the presence of clonal chromosome anomalies: interstitial deletion of the long arm of chromosome 20 (five cases), isochromosome of the long arm of chromosome 7 (one case), other anomalies (two cases). The study was performed by microarray technique considering the whole transcriptome (WT), and three gene subsets, selected as relevant in BM functions. The results were compared with those of nine patients with SDS without clonal anomalies, and of nine healthy subjects. There is a significant difference between gene expression in BM of SDS patients and healthy subjects, both at level of WT and of the gene sets selected. The deletion del(20)(q), with the EIF6 gene consistently lost, even in patients with the smallest losses of material, changes the transcription pattern: a low proportion of abnormal cells lead to a pattern similar to SDS patients without acquired anomalies, whereas a high proportion yields to a pattern similar to healthy subjects. Hence, the benign prognostic value of the del(20)(q). The case of i(7)(q10) showed a transcription pattern similar to healthy subjects, paralleling the positive prognostic role of this anomaly as well.