In recent years, tremendous effort has been spent to modernizing communication infrastructure in Cyber-Physical Systems (CPS) such as Industrial Control Systems (ICS) and related Supervisory Control and Data Acquisition (SCADA) systems. While a great amount of research has been conducted on network security of office and home networks, recently the security of CPS and related systems has gained a lot of attention. Unfortunately, real-world CPS are often not open to security researchers, and as a result very few reference systems and topologies are available. In this work, we present MiniCPS, a CPS simulation toolbox intended to alleviate this problem. The goal of MiniCPS is to create an extensible, reproducible research environment targeted to communications and physical-layer interactions in CPS. MiniCPS builds on Mininet to provide lightweight real-time network emulation, and extends Mininet with tools to simulate typical CPS components such as programmable logic controllers, which use industrial protocols (Ethernet/IP, Modbus/TCP). In addition, MiniCPS defines a simple API to enable physical-layer interaction simulation. In this work, we demonstrate applications of MiniCPS in two example scenarios, and show how MiniCPS can be used to develop attacks and defenses that are directly applicable to real systems.