Heparins have been shown to be beneficial for the prevention of habitual miscarriages and repeated implantation failure, independently of their function as anticoagulants. The pro-inflammatory cytokine tumor necrosis factor (TNF)-α plays a role in the pathogenesis of these early pregnancy complications. Therefore, we examined the impact of heparin on TNF-α signaling in human endometrial stromal cells (ESCs) in vitro. Human ESCs were isolated from hysterectomy specimens and either used as undifferentiated cells or after decidualization in vitro. Cells were incubated with TNF-α, unfractionated heparin and signaling- and transporter-inhibitors. Interleukin (IL)-8 and -6 were measured using ELISAs and real-time RT-PCR. Nuclear factor of transcription (NF)-κB and its inhibitor IκBα were analyzed by in-cell western assays and confocal microscopy. Activation of NF-κB was determined in nuclear extracts using a specific transcription factor assay. Cellular internalization of heparin was detected by a heparin-uptake assay. Unfractionated heparin significantly suppressed the TNF-α-induced and NF-κB-mediated secretion and expression of IL-8 and -6 as well as other molecules in decidualized and undifferentiated human ESCs. Thereby heparin had no influence on the degradation of IκBα and the phosphorylation of NF-κB, but it inhibited the activity of NF-κB in the nucleus. An active heparin-uptake into the cells was the prerequisite for these heparin-effects. Unfractionated heparin is able to inhibit TNF-α/NF-κB-mediated inflammatory effects in the human endometrium independently of its classical function as an anticoagulant. These observations further underline on a molecular level the beneficial anti-inflammatory effects of heparin in women suffering from implantation disorders even in the absence of a thrombophilia.