Cyclic thrombocytopenia (CTP) is a rare disorder characterized by periodic changes in platelet count. While some previous reports suggest an association with several cytokines, the etiology of this disorder remains poorly characterized. Using DNA microarrays, we examined the gene expression profile in peripheral whole blood at multiple time points encompassing a cycle of platelet counts from two CTP patients. We hypothesized that the variation in gene expression program in whole blood would reflect on the transcriptional changes associated with or perhaps even underlying this disease. Genome-wide cDNA microarray analysis was performed using amplified RNA obtained from 11 and 8 whole blood samples from each patient. The first patient is a 41-year old male with a 2-year history of CTP while the second patient is a 54-year old male with a 3-year history of CTP. The period of both patients’ cycles is roughly 3 weeks. No associated underlying disease has been found in both patients. With a focus on 1500 genes that change 3 fold within each group of samples we observed clusters of gene expression in whole blood that correlate with changing platelet numbers in both patients. Significant variation in expression of a cluster of interferon responsive genes during the platelet count cycle was particularly striking in both samples. Interferon (IFN) therapy is known to suppress platelet counts, and this observation suggests that aberrant IFN levels and signalling could be in part responsible for CTP. At high platelet counts, platelet transcripts were detected in whole blood RNA as inferred by high expression of previously described platelet genes including TBXAS1, TUBB1, OAZ1, SEPT5, several mitochondrial genes, NRGN and F13A1. In addition, gene clusters including known genes as well as previously uncharacterized genes were found to correlate with the peak, increasing or decreasing trends of platelet counts. Briefly, GATA2 and NFE2 expression coincided with the platelet count peak, while Tyk2 and SOCS5 expression was consistent with a rising trend of platelet counts and GATA3 and JAK2 coincided with decreasing trend of platelet counts. These results show gene expression changes associated with CTP in all cell types in whole blood and pave the way for new investigation into regulation of platelet number in a rare and fascinating disease.