Purpose Gene expression profiling (GEP) has demonstrated utility in identifying heart transplant (HTx) patients at increased risk for acute rejection (AR) in adult populations. GEP has not been well studied in pediatric HTx patients whose immune system function may differ from adults. Improved understanding of alterations in gene expression between AR and quiescence may be beneficial in pediatric HTx recipients. Methods and Materials Blood samples were prospectively collected from pediatric HTx recipients (aged 1-18 years) who had undergone transplant at least six months prior to enrollment. Samples were collected over one year, at six month intervals and at time of AR. Acute rejection was defined as clinically indicated augmentation of immunosuppression which in some patients was accompanied by abnormal echocardiogram or biopsy. GEP of 84 genes in the inflammatory cascade (chemokines, cytokines and their receptors) was performed on peripheral mononuclear lymphocytes by commercially available PCR (Illumina Biosciences) array. Expression profiles were analyzed with the commonly used Significant Analysis of Microarray (SAM). Comparison was within individual at time of AR and quiescence. The genes that differentially expressed with and without AR were identified by controlling the false discovery rates at 5%. Results Gene expression profiling was conducted on 17 blood samples (AR and quiescent) from five subjects. A total of 47331 transcripts from the 84 genes were analyzed. Expression levels of defensin family of genes were significantly higher at the time of at AR than at the time of quiescence. This pattern was consistent in 3 of 5 subjects. Conclusions Gene expression profiling holds promise in identifying specific regulatory pathways or gene families with differential activity at times of AR in pediatric HTx recipients. The gene family identified in this study is different from those identified in adult HTx recipients. Further study could lead to improved ability to modulate immunosuppression and/or predict impending AR.