Fetal growth restriction (FGR), a clinically significant pregnancy disorder, is poorly understood at the molecular level. This study investigates idiopathic FGR associated with placental insufficiency. Previously, we showed that the homeobox gene HLX is expressed in placental trophoblast cells and that HLX expression is significantly decreased in human idiopathic FGR. Here, we used the novel approach of identifying downstream targets of HLX in cell culture to detect potentially important genes involved in idiopathic FGR. Downstream targets were revealed by decreasing HLX expression in cultured trophoblast cells with HLX-specific small interfering RNAs to model human idiopathic FGR and comparing these levels with controls using a real-time PCR-based gene profiling system. Changes in candidate HLX target mRNA levels were verified in an independent trophoblast cell line, and candidate target gene expression was assessed in human idiopathic FGR-affected placentae (n = 25) compared with gestation-matched controls (n = 25). The downstream targets RB1 and MYC, cell cycle regulatory genes, showed significantly increased mRNA levels in FGR-affected tissues compared with gestation-matched controls, whereas CCNB1, ELK1, JUN, and CDKN1 showed significantly decreased mRNA levels (n = 25, P < 0.001, t-test). The changes for RB1 and CDKN1C were verified by Western blot analysis in FGR-affected placentae compared with gestation-matched controls (n = 6). We conclude that cell cycle regulatory genes RB1, MYC, CCNB1, ELK1, JUN, and CDKN1C, which control important trophoblast cell functions, are targets of HLX.